Academic YEAR 2018

Date Speaker 1 Speaker 2 Details
9/26/17 Orientation
10/3/17 Andrew Natale (Biophysics) Daniel Schwarz (CCB)

Andrew Natale (Biophysics)

Global analysis of protein folding using massively parallel design, synthesis, and testing

Rocklin et al., Science 357, 168–175 (2017)

http://science.sciencemag.org/content/357/6347/168

Daniel Schwarz (CCB)

b2-Adrenoreceptor is a regulator of the a-synuclein gene driving risk of Parkinson’s disease.

Mittal S. et al. b2-Adrenoreceptor is a regulator of the a-synuclein gene driving risk of Parkinson’s disease. Science. 2017; 357(6354):891-898.

http://science.sciencemag.org/content/357/6354/891.full

10/10/17 Jason Town (Bioinformatics) Serena Tamura

Jason Town (Bioinformatics)

DNA Cross-Bridging Shapes a Single Nucleus from a Set of Mitotic Chromosomes

Samwer, M et al. Cell, 170(5), 956–972.e23.

https://doi.org/10.1016/j.cell.2017.07.038

Serena Tamura

Correction of a pathogenic gene mutation in human embryos

Ma H et al. Nature 548, pp. 413–419 (24 August 2017).

http://www.nature.com/nature/journal/v548/n7668/full/nature23305.html

10/17/17 Emma Hughes Alison Maxwell (CCB)

Emma Hughes

Using geospatial mapping to design HIV elimination strategies for sub-Saharan Africa

Coburn et al. Science Translational Medicine, Vol. 9, Issue 383 (29 Mar 2017).

http://stm.sciencemag.org/content/9/383/eaag0019/tab-pdf

Alison Maxwell (CCB)

Single methyl groups can act as toggle switches to specify transmembrane protein-protein interactions

Li H. et al. eLife (4September 2017).

https://www.ncbi.nlm.nih.gov/pubmed/28869036

10/24/17 Peter Rohweder (CCB) Matvei Khoroshkin (Bioinformatics)

Peter Rohweder (CCB)

Global survey of the immunomodulatory potential of common drugs.

Vladimer, G. I. et al. Nat. Chem. Biol. 13, 681–690 (2017).

https://www.ncbi.nlm.nih.gov/pubmed/28437395

Matvei Khoroshkin (Bioinformatics)

Complex cellular logic computation using ribocomputing devices

Green, A. A. et al. Nature 548, 117–121 (3 August 2017).

http://www.nature.com/nature/journal/v548/n7665/full/nature23271.html?foxtrotcallback=true

10/31/17 Justin Jenkins Kevin Lou (CCB)

Justin Jenkins

Sensory neurons co-opt classical immune signaling pathways to mediate chronic itch.

Oetjen, Landon K., et al. Cell 171.1: 217-228 (2017).

Sensory neurons co-opt classical immune signaling pathways to mediate chronic itch.

Kevin Lou (CCB)

Probing the roles of SUMOylation in cancer cell biology by using a selective SAE inhibitor

He, X. et al. Nat Chem Biol (2017).

https://www.nature.com/articles/nchembio.2463

11/7/17 Sophia Tan (Biophysics) Taia Wu (CCB)

Sophia Tan (Biophysics)

Discovery of a cryptic peptide-binding site on PCSK9 and design of antagonists

Zhang Y. et al. Nature Structural & Molecular Biology 24, 848–856 (21 August 2017).

https://www.nature.com/nsmb/journal/v24/n10/full/nsmb.3453.html

Taia Wu (CCB)

Structures of the human mitochondrial ribosome in native states of assembly.

Brown, Alan, et al. Nature structural & molecular biology (2017).

https://www.nature.com/nsmb/journal/v24/n10/pdf/nsmb.3464.pdf

11/14/17 Beatrice Ary (CCB) Marcus Chin

Beatrice Ary (CCB)

Mapping Protein Targets of Bioactive Small Molecules Using Lipid-Based Proteomics

Lum K et al. ACS Chemical Biology, 12 (10), pp 2671–2681(20 September 2017).

http://pubs.acs.org/doi/abs/10.1021/acschembio.7b00581

Marcus Chin

Tau Prion Strains Dictate Patterns of Cell Pathology, Progression Rate, and Regional Vulnerability In Vivo

Kaufman S et al. Neuron Volume 92, Issue 4, Pages 796-812 (23 November 2016).

http://www.sciencedirect.com/science/article/pii/S0896627316306973?via%3Dihub

11/28/17 Susanna Elledge (CCB) Taylor Arhar (CCB)

Susanna Elledge (CCB)

Antibody-powered nucleic acid release using a DNA-based nanomachine

Ranallo et al. Nature Communications 8, 15150 (08 May 2017).

https://www.nature.com/articles/ncomms15150.pdf

Taylor Arhar (CCB)

Polypharmacology-based ceritinib repurposing using integrated functional proteomics

Kuenzi BM et al. Nature Chemical Biology (09 October 2017).

https://www.nature.com/articles/nchembio.2489?WT.feed_name=subjects_biotechnology

12/5/17 Reid Kinser Cynthia Chio (CCB)

Cynthia Chio (CCB)

The condensin complex is a mechanochemical motor that translocates along DNA.

Terakawa T et al. Science 358 (6363):672-676 (3 Nov 3 2017).

https://www.ncbi.nlm.nih.gov/pubmed/28882993

12/12/17 Bianca Vora Douglas Wassarman (CCB)
1/9/18 Wesley Marin (Biophysics) Adam Melgoza

Adam Melgoza

Non-steroidal Anti-inflammatory Drugs are Caspase Inhibitors

Smith C et al. Cell Chemical Biology 24, 281-292 (2017 March 16).

http://www.cell.com/cell-chemical-biology/pdf/S2451-9456(17)30033-8.pdf

1/16/18 Lisa Kirkemo (CCB) Jeffrey Kim
1/23/18 Albert Dai (CCB) Arielle Shkedi
1/30/18 Keely Oltion (CCB) Kaitlyn Tsai (CCB)
2/6/18 Paul Klauser (CCB) Lakshmi Miller-Vedam
2/13/18 Julian Harris (CCB) Dina Buitrago-Silva
2/20/18 Kelly Montgomery (CCB) Christa Caggiano
2/27/18 Jean Costello Chase Webb
3/6/18 Eric Gonzalez (CCB) Maureen Pittman
3/13/18 Megan Whalen Jack Stevenson (CCB)
3/20/18 Matthew Jones Adam Cotton (CCB)
3/27/18 Snow Naing Paige Solomon (CCB)
4/3/18 Capria Rinaldi Daniel Wong
4/10/18 Neha Prasad (CCB) Erik Navarro
4/17/18 Jenna Pellegrino Tia Tummino
4/17/18 Andrew Kung
4/24/18 Annamarie Bustion Nishith Reddy
4/24/18 Yessica Gomez
5/1/18 Megan Moore (CCB) Jared Lumpe
5/1/18 Megan Koleske
5/8/18 Benjamin Catching Nicole Wenzell
5/15/18 Mikayla Richter Kyle Lopez
5/22/18 Viktoriya Berdan (CCB) Taylor Cavazos
5/29/18 George Hartoularos Ki Kim
6/5/18 Andrew Natale (Biophysics) Colton Bracken (CCB)
6/12/18 Conner Bardine (CCB) Mary Gordon

Academic YEAR 2017

Date Speaker 1 Speaker 2 Details
9/27/16 Orientation
10/4/16 Nick Rettko (CCB) Nadja Kern (Biophysics)

Nick Rettko (CCB)

Structural Basis of Zika Virus-Specific Antibody Protection

Zhao, H. & Fernandez, E. et al. Cell. August 11, 2016

http://www.cell.com/cell/pdfExtended/S0092-8674(16)30927-8

Nadja Kern (Biophysics)

Phosphotyrosine-mediated LAT assembly on membranes drives kinetic bifurcation in recruitment dynamics of the Ras activator SOS

Huang, W. Y. C., et al. PNAS vol. 113 no. 29 pp. 8218–8223 (2016).

http://doi.org/10.1073/pnas.1602602113http://

10/11/16 Michael Song Daniel Asarnow (Bioinformatics)

Michael Song

Inhibition of Dihydroorotate Dehydrogenase Overcomes Differentiation Blockade in Acute Myeloid Leukemia.

Sykes DB et al, Cell Volume 167(1), pp. 171-186 (September 22, 2016).

https://www.ncbi.nlm.nih.gov/pubmed/27641501

Daniel Asarnow (Bioinformatics)

How to Distinguish Conformational Selection and Induced Fit Based on Chemical Relaxation Rates

Paul F et al. PLoS Comput. Biol. vol. 12, no. 9 (September 2016).

http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005067

10/18/16 Ruilin Tian (Biophysics) Ryan Tibble (CCB)

Ruilin Tian (Biophysics)

Synchronized cycles of bacterial lysis for in vivo delivery

Din, MO et al. Nature volume 536 (7614), pp. 81-85 (20 July 2016).

http://www.nature.com/nature/journal/v536/n7614/full/nature18930.html

Ryan Tibble (CCB)

m6A RNA methylation promotes XIST-mediated transcriptional repression

Patil DP et al. Nature 537 (7620):369-373 (2016 Sep 7).

http://www.nature.com/nature/journal/v537/n7620/full/nature19342.html

10/25/16 Kathleen Keough Charlotte Nelson (Bioinformatics)

Kathleen Keough

The Simons Genome Diversity Project: 300 genomes from 142 diverse populations

Mallick, S. et al. Nature doi:10.1038/nature18964 (21 September 2016).

http://www.nature.com/nature/journal/vaop/ncurrent/full/nature18964.html

Charlotte Nelson (Bioinformatics)

Amoebas, ETs, & Evolution

Zhang, X et al. Social amoebae trap and kill bacteria by casting DNA nets. Nature (1 March 2016).

http://www.nature.com/articles/ncomms10938

11/1/16 Rachel Brunetti (Biophysics) Mikhail Vysotskiy

Rachel Brunetti (Biophysics)

Phase Transition in Postsynaptic Densities Underlies Formation of Synaptic Complexes and Synaptic Plasticity.

Zeng, M. et al. Cell, 166(5), 1163-1175 (25 August 2016).

http://www.cell.com/cell/pdf/S0092-8674(16)30914-X.pdf

Mikhail Vysotskiy

Analysis of protein-coding genetic variation in 60,706 humans

Lek M. et al. Nature 536, 285–291 (18 August 2016).

http://www.nature.com/nature/journal/v536/n7616/full/nature19057.html

11/8/16 Paul Thomas (Biophysics) Emmalyn Chen

Paul Thomas (Biophysics)

Why so Blue?: Selection for iridescence in plants.

Jacobs, et al. Photonic multilayer structure of Begonia chloroplasts enhances photosynthetic efficiency. Nature Plants Article number: 16162 (24 October 2016).

http://www.nature.com/articles/nplants2016162

Emmalyn Chen

Cell-free DNA Comprises an In Vivo Nucleosome Footprint that Informs Its Tissues-Of-Origin

Snyder, M. W. et al. Cell Vol. 164, Issues 1-2, pp. 57–68 (14 January 2016).

http://www.cell.com/abstract/S0092-8674(15)01569-X

11/15/16 Emily Kang (CCB) Beau Norgeot

Emily Kang (CCB)

A Genome-wide CRISPR Screen in Toxoplasma Identifies Essential Apicomplexan Genes

Salma S. M. et al. Cell. 2016. 166(6): 1423-1435.

http://www.sciencedirect.com/science/article/pii/S0092867416310704

Beau Norgeot

An Unsupervised Representation to Predict the Future of Patients from the Electronic Health Records

Miotto R et al. Scientific Reports 6, Article number: 26094 (17 May 2016).

http://www.nature.com/articles/srep26094

11/22/16 Tamas Nagy (Bioinformatics) Yuliya Birman (Biophysics)

Tamas Nagy (Bioinformatics)

You’re just a number: New methods for bibliometric assessment of scientific productivity

Relative Citation Ratio (RCR): A New Metric That Uses Citation Rates to Measure Influence at the Article Level (PLoS Biology, September 2016)

http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1002541

Yuliya Birman (Biophysics)

Molecular basis for multimerization in the activation of the epidermal growth factor receptor.

Huang, Y. et al. eLife DOI: http://dx.doi.org/10.7554/eLife.14107 (28 March 2016)

https://elifesciences.org/content/5/e14107

11/29/16 Derek Britain (Biophysics) Julia Cluceru

Derek Britain (Biophysics)

A Screen for Protein Based Memory

Chakrabortee, S. et al. Intrinsically Disordered Proteins Drive Emergence and Inheritance of Biological Traits. Cell Volume 167, Issue 2, pp. 369–381.e12 (6 October 2016).

http://www.cell.com/cell/abstract/S0092-8674(16)31250-8

Julia Cluceru

NAD⁺ repletion improves mitochondrial and stem cell function and enhances life span in mice

Zhang H et al. Science 352 (6292):1436-43. doi: 10.1126/science.aaf2693. PubMed PMID: 27127236. (2016 Jun 17).

https://www.ncbi.nlm.nih.gov/pubmed/27127236

12/6/16 Elizabeth Levy Fatima Ugur (CCB)

Elizabeth Levy

Magneto-aerotactic bacteria deliver drug-containing nanoliposomes to tumour hypoxic regions

Felfoul, O et al. Nature Nanotechnology, 11 pp. 941–947 (15 August 2016).

http://www.nature.com/nnano/journal/v11/n11/full/nnano.2016.137.html

Fatima Ugur (CCB)

Arginine phosphorylation tagging system for proteolysis in bacteria

Trentini et al. Arginine phosphorylation marks proteins for degradation by a Clp protease. Nature, 539, 48-53 (3 November 2016).

http://www.nature.com/nature/journal/v539/n7627/full/nature20122.html

1/10/17 Nat Hendel (Bioinformatics) Sergei Pourmal (CCB)

Nat Hendel (Bioinformatics)

Vortex Arrays and Ciliary Tangles Underlie the Feeding-Swimming Trade-off in Starfish Larvae

Gilpin W et al. Nature Physics advance online publication (December 19, 2016).

http://www.nature.com/nphys/journal/vaop/ncurrent/full/nphys3981.html

Sergei Pourmal (CCB)

Potent, Reversible, and Specific Chemical Inhibitors of Eukaryotic Ribosome Biogenesis

Kawashima, S. A. et al.. Cell 167, 512–524.e14 (2016).

http://www.cell.com/cell/abstract/S0092-8674(16)31168-0

1/17/17 Jasleen Sodhi Cole Helsell (Biophysics)

Jasleen Sodhi

Lifestyle chemistries from phones for individual profiling

Bouslimani A et al. PNAS vol. 113 no. 48 E7645–E7654 (14 November 2016).

http://www.pnas.org/content/113/48/E7645.fullhttp://www.pnas.org/content/113/48/E7645.full

1/24/17 Pooja Suresh (Biophysics) Douglas Myers-Turnbull (Bioinformatics)

Pooja Suresh (Biophysics)

Mechanical plasticity of cells

Bonakdar N. et al. Nature Materials Vol 15, pp. 1090-1094 (4 July 2016).

http://www.nature.com/nmat/journal/v15/n10/full/nmat4689.html

Douglas Myers-Turnbull (Bioinformatics)

Network integration of parallel metabolic and transcriptional data reveals metabolic modules that regulate macrophage polarization.

Jha AK et al. Immunity 42 (3):419-30 (2015 Mar 17).

https://www.ncbi.nlm.nih.gov/pubmed/25786174

1/31/17 Alex Wolff (Biophysics) Marjorie Imperial

Alex Wolff (Biophysics)

Structure of protein O-mannose kinase reveals a unique active site architecture

Zhu et al.; eLife; Nov 23, 2016; DOI: 10.7554/eLife.22238

https://elifesciences.org/content/5/e22238

Marjorie Imperial

A Liver-Centric Musicale Modeling Framework for Xenobiotics

Sluka et al., PLoS One 11(9):e0162428 (16 Sep 2016).

http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0162428

2/7/17 David Bauer (Biophysics)

David Bauer (Biophysics)

Precise measurement of single cancer cell mass accumulation predicts drug susceptibility

Stevens MM et al. Nature Biotechnology 34, 1161–1167  (10 October 2016).

http://www.nature.com/nbt/journal/v34/n11/full/nbt.3697.html

2/14/17 Peter McTigue (CCB) Jeffrey Kim

Peter McTigue (CCB)

A synthetic ion transporter that disruptsautophagy and induces apoptosis by perturbingcellular chloride concentrations

Busschaert N et al. Nature Chemistry, 2017, Advance Online Publication (30 January 2017).

http://www.readcube.com/articles/10.1038/nchem.2706

Jeffrey Kim

CD4+ T-cell–independent mechanisms suppress reactivation of latent tuberculosis in a macaque model of HIV coinfection

Foreman et al., PNAS 113(38), September 6 2016, doi: 10.1073/pnas.1611987113

http://www.pnas.org/content/113/38/E5636.abstract

2/21/17 Cynthia Chio (CCB) Greyson Lewis

Cynthia Chio (CCB)

Cotranslational signal-independent SRP preloading during membrane targeting

Chartron, J. W. et al. Nature 536, 224-228 (11 August 2016).

http://www.nature.com/nature/journal/v536/n7615/full/nature19309.html

Greyson Lewis

Synthetic recombinase-based state machines in living cells

Roquet N et al. Science Vol. 353, Issue 6297 (22 Jul 2016).

http://science.sciencemag.org/content/353/6297/aad8559

2/28/17 Taia Wu (CCB) Bianca Vora

Taia Wu (CCB)

De novo design of a biologically active amyloid

Gallardo R et al. De novo design of a biologically active amyloid. Science Volume 354, Issue 6313 (11 November 2016).

http://science.sciencemag.org/content/354/6313/aah4949

Bianca Vora

Natural history of the infant gut microbiome and impact of antibiotic treatment on bacterial strain diversity and stability

Yassour M et al. Natural History of the Infant Gut Microbiome and Impact of Antibiotic Treatment on Bacterial Strain Diversity and Stability. Science Translational Medicine, 8, 343-381 (15 June 2016).

http://stm.sciencemag.org/content/8/343/343ra81

3/7/17 Kevin Lou (CCB) Gabe Reder

Kevin Lou (CCB)

Diversity-Oriented Synthesis Yields Novel Multistage Antimalarial Inhibitors

Kato, N. et al. Nature 538, 344–349 (2016).

http://www.nature.com/nature/journal/v538/n7625/full/nature19804.html

Gabe Reder

β-cell–mimetic designer cells provide closed-loop glycemic control

Xie M et al. Science Volume 354, Issue 6317 (09 December 2016).

http://science.sciencemag.org/content/354/6317/1296.full

3/14/17 Justin Jenkins Douglas Wassarman (CCB)

Justin Jenkins

A solution to the single-question crowd wisdom problem

Prelec D et al. Nature 541, 532–535 (26 January 2017).

http://www.nature.com/nature/journal/v541/n7638/full/nature21054.html

Douglas Wassarman (CCB)

Creating Interspecies Chimeras Using Pluripotent Stem Cells

Wu J, et al. Interspecies Chimerism with Mammalian Pluripotent Stem Cells. Cell 168(3):473-486 (2017 Jan 26).

http://www.cell.com/cell/abstract/S0092-8674(16)31752-4

3/21/17 Susanna Elledge (CCB) Adam Melgoza

Susanna Elledge (CCB)

Recurrent RNA motifs as scaffolds for genetically encodable small-molecule biosensors

Porter, E. et al. Nat Chem Biol. 13 , 295-301 (16 Jan 2017)

http://www.nature.com/nchembio/journal/v13/n3/full/nchembio.2278.html

Adam Melgoza

NMDAR inhibition-independent antidepressant actions of ketamine metabolites

Zanos P et al. Nature 533 (7604): 481-486 (04 May 2016).

http://www.nature.com/nature/journal/v533/n7604/full/nature17998.html

4/4/17 Kaitlyn Tsai (CCB) Emma Hughes

Kaitlyn Tsai (CCB)

Communication between viruses guides lysis–lysogeny decisions

Erez Z. et al. Nature 541, 488–493 (26 January 2017).

http://www.nature.com/nature/journal/v541/n7638/abs/nature21049.html

Emma Hughes

Inflammatory signaling in human tuberculosis granulomas is spatially organized

Marakala MJ et al. Nature Medicine 22, pp. 531–538 (4 April 2016).

http://www.nature.com/nm/journal/v22/n5/full/nm.4073.html

4/11/17 Jason Town Lisa Kirkemo (CCB)

Jason Town

Survey of variation in human transcription factors reveals prevalent DNA binding changes

Barrera, L. A. et al. Science volume 351, issue 6280, pp. 1450-1454 (25 March 2016).

http://http://science.sciencemag.org/content/351/6280/1450.abstract

Lisa Kirkemo (CCB)

Selective Small Molecule Inhibition of PCSK9 Translation

Petersen, D. et al. Cell Chemical Biology, 23 (11), 1362–1371 (17 November 2016).

https://www.ncbi.nlm.nih.gov/pubmed/27746128

4/18/17 Ian Bergman (CCB) Stella Belonwu

Ian Bergman (CCB)

Bactericidal Effects of Natural Nanotopography of Dragonfly Wing on Escherichia coli.

Bandara CD et al. ACS Appl Mater Interfaces, 9 (8): 6746-6760 (1Mar 2017).

https://www.ncbi.nlm.nih.gov/pubmed/28139904

Stella Belonwu

Drug regimens identified and optimized by output-driven platform markedly reduce tuberculosis treatment time

Lee BY et al. Nature Communications 8:14183 (24 January 2017).

http://www.nature.com/articles/ncomms14183

4/25/17 Daniel Schwarz (CCB) Serena Tamura

Daniel Schwarz (CCB)

Selective stalling of human translation through small-molecule engagement of the ribosome nascent chain

Lintner NG et al. PLoS Biol 15(3): e2001882 (21 March 2017).

http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.2001882

Serena Tamura

CHD8 haploinsufficiency results in autistic-like phenotypes in mice

Katayama Y et al. Nature Volume 537 pp. 675-693 (29 September 2016).

http://www.nature.com/nature/journal/v537/n7622/full/nature19357.html

5/2/17 Alison Maxwell (CCB)

Alison Maxwell (CCB)

Autocatalytic, bistable, oscillatory networks of biologically relevant organic reactions

Semenov S et al. Nature 537(7622):656-60 (September 2016).

http://www.nature.com/nature/journal/v537/n7622/full/nature19776.html

5/9/17 Keely Oltion (CCB) Reid Kinser

Keely Oltion (CCB)

Microbiota Diurnal Rhythmicity Programs Host Transcriptome Oscillations

Thaiss C et al. Cell 167, pp. 1495-1510 (1 December 2016).

http://www.cell.com/fulltext/S0092-8674(16)31524-0

Reid Kinser

α-Helix Mimetics as Modulators of Aβ Self-Assembly

Kumar S et al. Journal of the American Chemical Society 139 (16), 5744-5755 (12 April 2017).

https://www.ncbi.nlm.nih.gov/pubmed/28273416

5/16/17 Sophia Tan Sasha Dickenson (CCB)

Sophia Tan

Tardigrades Use Intrinsically Disordered Proteins to Survive Desiccation

Boothby TC et al. Molecular Cell Volume 65, Issue 6, pp. 975–984.e5 (16 March 2017).

http://www.sciencedirect.com/science/article/pii/S1097276517301338?np=y&npKey=cd8e11b46ae7ba9ed009a16d52801484533f6f3973b0c859268fe19234051dc3

Sasha Dickenson (CCB)

Experimental measurement of binding energy, selectivity, and allostery using fluctuation theorems

Camunas-Soler et al., Science 355, 412–415 (27 January 2017).

http://science.sciencemag.org/content/355/6323/412

5/23/17 Shizhong Dai (CCB) Arielle Shkedi

Shizhong Dai (CCB)

Redox-based reagents for chemoselective methionine bioconjugation

Lin S et al. Science Vol. 355, Issue 6325, pp. 597-602 (10 Feb 2017).

http://science.sciencemag.org/content/355/6325/597

Arielle Shkedi

Transient CDK4/6 inhibition protects hematopoietic stem cells from chemotherapy-induced exhaustion

He S et al. Science Translational Medicine Vol. 9, Issue 387, eaal 3986 (26 April 2017.

http://stm.sciencemag.org/content/9/387/eaal3986/tab-pdf

5/30/17 Wesley Marin (Bioinformatics) Beatrice Ary (CCB)

Wesley Marin (Bioinformatics)

Trade-off between Transcriptome Plasticity and Genome Evolution in Cephalopods

Liscovitch-Brauer, Noa et al. Cell , Volume 169 , Issue 2 , 191 - 202.e11 (6 April 2017).

http://www.cell.com/fulltext/S0092-8674(17)30344-6

Beatrice Ary (CCB)

A Vibrio cholerae autoinducer–receptor pair that controls biofilm formation

Papenfort K. et al. Nature Chemical Biology 13, 551–557 (20 March 2017).

https://www.nature.com/nchembio/journal/v13/n5/full/nchembio.2336.html

6/6/17 Taylor Arhar (CCB) Marcus Chin

Taylor Arhar (CCB)

Diabetes reversal by inhibition of the low-molecular-weight tyrosine phosphatase

Stanford S et al. Nature Chemical Biology Biology 13, 624–632 (27 March 2017).

http://www.nature.com/nchembio/journal/v13/n6/full/nchembio.2344.html#affil-auth

Marcus Chin

Caspase-2 cleavage of tau reversibly impairs memory

Zhao X et al. Nat Med. 22 (11): 1268-1276 (October 10 2016).

https://www.ncbi.nlm.nih.gov/pubmed/27723722

6/13/17 Peter Rohweder (CCB) Sasha Targ (Bioinformatics)

Peter Rohweder (CCB)

Defining B cell immunodominance to viruses

Angeletti, D. et al. Defining B cell immunodominance to viruses. Nat. Immunol. 18, 456–463 (13 February 2017).

http://www.nature.com/ni/journal/v18/n4/full/ni.3680.html

Sasha Targ (Bioinformatics)

Composite measurements and molecular compressed sensing for highly efficient transcriptomics

Cleary B et al. BioRxIV doi: https://doi.org/10.1101/091926 (2 January 2017).

http://biorxiv.org/content/early/2017/01/02/091926

6/13/17 Matvei Khoroshkin (Bioinformatics)

Matvei Khoroshkin (Bioinformatics)

Regulated Intron Removal Integrates Motivational State and Experience

Gill, Jason et al. Cell , Volume 169, Issue 5, 836 - 848.e15 (18 May 2017).

http://www.cell.com/cell/abstract/S0092-8674(17)30533-0

Academic YEAR 2016

Date Speaker 1 Speaker 2 Details
9/29/15 Orientation
10/6/15 Christine Bowman Steven Moss (CCB)

Christine Bowman

Microneedle-array patches loaded with hypoxia-sensitive vesicles provide fast glucose-responsive insulin delivery

Yu J et al. PNAS p. 8260–8265, vol. 112 no. 27 (May 19, 2015).

http://www.pnas.org/content/112/27/8260.abstract

Steven Moss (CCB)

Photoswitchable Inhibitors of Microtubule Dynamics Optically Control Mitosis and Cell Death

Borowiak, M. et. al. Cell 162: 2, 403-411 (July 2015).

http://www.cell.com/cell/abstract/S0092-8674%2815%2900774-6

10/13/15 Reed Stein Stefan Niekamp (Biophysics)

Reed Stein

Disease-associated mutation in SRSF2 misregulates splicing by altering RNA-binding affinities

Zhang et al. PNAS Vol. 112 no. 34 E4726-4734 (10 August 2015)

http://www.pnas.org/content/112/34/E4726/F2.expansion.html

Stefan Niekamp (Biophysics)

Ribosome Excursions during mRNA Translocation Mediate Broad Branching of Frameshift Pathways

Yan S. et al. Cell Volume 160, Issue 5, p870–881 (26 February 2015).

http://www.cell.com/cell/abstract/S0092-8674%2815%2900136-1

10/20/15 Kaitlin Hulce (CCB) Hayley Donnella

Kaitlin Hulce (CCB)

An excess of catalytically required motions inhibits the scavenger decapping enzyme

Neu A et al. Nat. Chem. Bio. 2015, 11 697-704.

http://www.readcube.com/articles/10.1038%2Fnchembio.1866

Hayley Donnella

Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets

Macosko EZ, et al. Cell 161(5):1202-14 (May 2015).

http://www.cell.com/abstract/S0092-8674(15)00549-8

10/27/15 Darya Cheng Weiyue Ji (Biophysics)

Darya Cheng

β2-microglobulin is a systemic pro-aging factor that impairs cognitive function and neurogenesis

Smith L et al. Nature Medicine 21,932–937 (2015).

http://www.nature.com/nm/journal/v21/n8/full/nm.3898.html

Weiyue Ji (Biophysics)

Gene transfer in complex cells

C. Ku et al., Endosymbiotic origin and differential loss of eukaryotic genes. Nature. 524, 427–432 (2015).

http://www.nature.com/nature/journal/v524/n7566/full/nature14963.html

11/3/15 Stephanie See (CCB)

Stephanie See (CCB)

Amyloid control of gametogenesis

Berchowitz, L. E. et al. Regulated Formation of an Amyloid-like Translational Repressor Governs Gametogenesis. Cell, 1–14 (2015).

11/10/15 Tyler Ross (Biophysics) Chimno Nnadi (CCB)

Tyler Ross (Biophysics)

Topology and dynamics of active nematic vesicles

Keber FC, et al. Science. Vol. 345 no. 6201 pp. 1135-1139 (2014 Sep 5).

http://www.sciencemag.org/content/345/6201/1135.short

Chimno Nnadi (CCB)

Noninvasive Brain Cancer Imaging with a bispecific antibody fragment generated via click chemistry.

Luo H et al. PNAS 2015 112 (41) 12806-12811; published ahead of print September 28, 2015.

http://www.pnas.org/content/112/41/12806.full.pdf

11/17/15 Megan Lo Seth Axen (Bioinformatics)

Megan Lo

Spatiotemporal control of β2AR signaling via optogenetic mutant

Optodynamic stimuation of β-adrenergic receptor signalling. Nature Communications. 2015 Sep 28. 6:8480.

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4588095/

Seth Axen (Bioinformatics)

Recurrent Domestication by Lepidoptera of Genes from Their Parasites Mediated by Bracoviruses

Gasmi L et al. PLoS Genetics. 2015 Sep 17.

http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1005470

11/24/15 Marco Mravic (Biophysics) Allison Wong (CCB)

Marco Mravic (Biophysics)

Native structure enables a synthetic mimic of Photosystem II water oxidation machinery: Why you might bump into Elon Musk at the XFEL

Zhang, C. et al. A synthetic Mn4Ca-cluster mimicking the oxygen-evolving center of photosynthesis. Science, 348(6235), 690-693 (2015).

https://www.sciencemag.org/content/348/6235/690.full

Allison Wong (CCB)

Arms race: A bacterial factor inactivates the bactericidal protein Perforin-2

McCormack, R. et al. Enteric pathogens deploy cell cycle inhibiting factors to block the bactericidal activity of Perforin-2. eLife 2015;10.7554/eLife.06505 (29 September 2015).

http://dx.doi.org/10.7554/eLife.06505

12/1/15 Ryan Muir (CCB) Katherina Chua

Ryan Muir (CCB)

Determinants of amyloid fibril degradation by the PDZ protease HTRA1

Poepsel et. al. Nat Chem Bio 11, 862-869 (Oct 2015)

http://www.nature.com/nchembio/journal/v11/n11/full/nchembio.1931.html

Katherina Chua

RNA-seq of tumor-educated platelets enables blood-based pan-cancer, multiclass, and molecular pathway cancer diagnostics

Best, M et al. Cancer Cell Volume 28, Issue 5, p666–676, 9 (November 2015).

http://www.cell.com/cancer-cell/abstract/S1535-6108%2815%2900349-9

12/8/15 Elena Caceres (Bioinformatics) Erin Poss (CCB)

Elena Caceres (Bioinformatics)

“Function-First” Lead Discovery: Mode of Action Profiling of Natural Product Libraries Using Image-Based Screening

Schulze CJ et al. Chemistry & Biology, Volume 20, Issue 2 (21 February 2013).

http://www.ncbi.nlm.nih.gov/pubmed/23438757

Erin Poss (CCB)

The evolutionary expansion of terpene synthases: to cyclize or not to cyclize?

Salmon et al. Emergence of terpene cyclization in Artemisia annua. Nature Communications. 10.1038/ncomms7143. (03 February 2015).

http://www.nature.com/ncomms/2015/150203/ncomms7143/abs/ncomms7143.html

1/5/16 Bruk Mensa (CCB) Eugene Palovcak (Biophysics)

Bruk Mensa (CCB)

Brain tumor cells interconnect to a functional and resistant network

Matthias Osswald et al. Nature 528, 93–98, 03 December 2015.

http://www.nature.com/nature/journal/v528/n7580/full/nature16071.html

Eugene Palovcak (Biophysics)

Mapping Nucleosome Resolution Chromosome Folding in Yeast by Micro-C

Hsieh et al. "Mapping Nucleosome Resolution Chromosome Folding in Yeast by Micro-C." Cell. (2015). Vol. 162-1. p108-109.

http://www.sciencedirect.com/science/article/pii/S0092867415006388

1/12/16 Leanna Morinishi (Bioinformatics) Lillian Kenner (Biophysics)

Leanna Morinishi (Bioinformatics)

Novel antibody-anbiotic conjugate eliminates intracellular S. aureus

Lehar, S.M., et al., Nature. 19 November 2015.

http://www.nature.com/nature/journal/v527/n7578/full/nature16057.html

Lillian Kenner (Biophysics)

Structural Basis of Vesicle Formation at the Inner Nuclear Membrane

Hagen et al., 2015, Cell 163, 1692–1701 December 17, 2015.

http://www.cell.com/cell/abstract/S0092-8674%2815%2901548-2

1/19/16 Evan Green (Biophysics) Adolfo Cuesta (CCB)

Evan Green (Biophysics)

Conformational dynamics of a class C G-protein-coupled receptor.

R Vafabakhsh, J Levitz and EY Isacoff. Nature 2015

http://www.nature.com/nature/journal/v524/n7566/full/nature14679.html

Adolfo Cuesta (CCB)

Acceleration of diabetic wound healing using a novel protease-anti protease combination therapy

Gao M et al. PNAS, December 18th 2015.

http://www.pnas.org/content/112/49/15226.abstract

1/26/16 Jessica Enogieru Rachel Gate (Bioinformatics)

Jessica Enogieru

Genome-wide analysis of human global and transcription-coupled excision repair of UV damage at single-nucleotide resolution

Hu J et al. GENES & DEVELOPMENT 29:948 – 960 (6 April 2015).

http://genesdev.cshlp.org/content/29/9/948.full.pdf+html

Rachel Gate (Bioinformatics)

Thousands of novel translated open reading frames in humans inferred by ribosome footprint profiling

Raj, A. et al. Thousands of novel translated open reading frames in humans inferred by ribosome footprint profiling. bioRxiv (2015).

http://biorxiv.org/content/early/2015/11/13/031617

2/2/16 Jasper Williams Meena Subramaniam (Bioinformatics)

Meena Subramaniam (Bioinformatics)

Predicting the impact of regulatory variants from DNA sequence

Lee D, Gorkin DU, Baker M, Strober BJ, Asoni AL, McCallion AS, et al. A method to predict the impact of regulatory variants from DNA sequence. Nat Genet. Nature Publishing Groupd; 2015 Aug 1;47(8):955–61.

http://www.nature.com/ng/journal/v47/n8/full/ng.3331.html

2/9/16 Eugenia Salcedo (CCB) Ina Chen (Bioinformatics)

Eugenia Salcedo (CCB)

PQBP1 Is a Proximal Sensor of the cGAS-Dependent Innate Response to HIV-1

Yoh, Sunnie M. et al. Cell , Volume 161 , Issue 6 , 1293 - 1305 (June 2015).

http://www.cell.com/abstract/S0092-8674%2815%2900525-5

Ina Chen (Bioinformatics)

Emergence of collective modes from epithelial confinement.

Deforet M. et al. Nature Comm 5, 3747 (6 May 2014).

http://www.nature.com/ncomms/2014/140506/ncomms4747/full/ncomms4747.html

2/16/16 Derek Britain Kathleen Keough

Derek Britain

A Hierarchical Multi-oscillator Network Orchestrates the Arabidopsis Circadian System

Takahashi N. et al. Cell Volume 163, Issue 1, p148–159 (24 September 2015).

http://www.cell.com/cell/abstract/S0092-8674%2815%2901114-9

Kathleen Keough

High-fidelity CRISPR-Cas 9 nucleases with no detectable genome-wide off-target effects

Kleinstiver, B. P. et al. High-fidelity CRISPR–Cas9 nucleases with no detectable genome-wide off-target effects. Nature (6 January 2016).

http://www.nature.com/nature/journal/vaop/ncurrent/full/nature16526.html

2/23/16 Nathan Hendel Peter McTigue (CCB)

Nathan Hendel

Harvester ants use interactions to regulate forager activation and availability

Pinter-Wollman, N. et al. Animal Behaviour 86, 197-207 ((2013).

http://www.sciencedirect.com/science/article/pii/S0003347213002133

Peter McTigue (CCB)

CRISPR-Cas9-based Photoactivatable Transcription System

Nihongaki Y et al. Chemistry & Biology Volume 22, Issue 2, p. 169–174 (19 February 2015).

http://www.sciencedirect.com.ucsf.idm.oclc.org/science/article/pii/S1074552114004591

3/1/16 Pooja Suresh Julia Cluceru

Pooja Suresh

Imaging G protein-coupled receptors while quantifying their ligand-binding free-energy landscape"

Alsteens D et al. Nature Methods 12, 845–851 (13 July 2015).

http://www.nature.com/nmeth/journal/v12/n9/full/nmeth.3479.html

Julia Cluceru

Whole genomes redefine mutational landscape of pancreatic cancer

Waddell N et al. Nature 518, 495–501 (26 February 2015).

http://www.nature.com/nature/journal/v518/n7540/abs/nature14169.html

3/8/16 Yuliya Birman (Biophysics) Daniel Asarnow (Bioinformatics)

Yuliya Birman (Biophysics)

Super-resolution imaging reveals distinct chromatin folding for different epigenetic states

Boettiger A.N., et al. Nature, 529, pp. 1-15 (21 January 2016).

http://www.nature.com/nature/journal/v529/n7586/full/nature16496.html

Daniel Asarnow (Bioinformatics)

Parallel computation with molecular-motor-propelled agents in nanofabricated networks

Nicolau DV et al. PNAS, p. 201510825 (Feb. 2016).

http://www.pnas.org/content/early/2016/02/17/1510825113.full

3/29/16 Nicholas Rettko (CCB) Alexander Wolff

Nicholas Rettko (CCB)

The Protease Ste24 Clears Clogged Translocons

Ast T. et al. Cell Volume 164, Issues 1-2, p103–114, 14 (January 2016).

http://www.cell.com/cell/abstract/S0092-8674%2815%2901572-X

Alexander Wolff

Cyanobacteria use micro-optics to sense light direction

Schuergers et al.; eLife; February 9, 2016

http://elifesciences.org/content/5/e12620v1

4/5/16 Ryan Tibble (CCB) Elizabeth Levy

Ryan Tibble (CCB)

Light-controlled modulation of gene expression by chemical optoepigenetic probes

Reis, S et al. Nature Chemical Biology (March 14, 2016).

http://www.nature.com/nchembio/journal/vaop/ncurrent/pdf/nchembio.2042.pdf

Elizabeth Levy

A photoactivable multi-inhibitor nanoliposome for tumour control and simultaneous inhibition of treatment escape pathways

Spring, B et al. Nature Nanotechnology (2016)

http://www.nature.com/nnano/journal/vaop/ncurrent/full/nnano.2015.311.html

4/12/16 Ruilin Tian (Biophysics) Sergei Pourmal (CCB)

Ruilin Tian (Biophysics)

A magnetic protein biocompass

Can Xie et al. Nature Materials, 15, 217-226 (2016).

www.nature.com/nmat/journal/v15/n2/full/nmat4484.html

Sergei Pourmal (CCB)

Cytotoxic T Cells Use Mechanical Force to Potentiate Target Cell Killing

Basu, R. et al. Cell 165, 100–110 (2016).

http://www.cell.com/cell/abstract/S0092-8674%2816%2900061-1

4/19/16 Marjorie Imperial Tamas Nagy

Marjorie Imperial

Personalized Nutrition by Prediction of Glycemic Responses

Zeevi, D et al. Cell Volume 163, Issue 5, p1079–1094 (19 November 2015).

http://www.cell.com/cell/fulltext/S0092-8674(15)01481-6

Tamas Nagy

Decreasing-Rate Pruning Optimizes the Construction of Efficient and Robust Distributed Networks

Navlakha S et al. PLOS Computational Biology (2015 July 28).

http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004347

4/26/16 Nadja Kern Beau Norgeot

Nadja Kern

De Novo Evolutionary Emergence of a Symmetrical Protein Is Shaped by Folding Constraints

Smock, R. et al. Cell 164.3 (2016): 476-86.

http://www.cell.com/cell/abstract/S0092-8674%2815%2901688-8

Beau Norgeot

The phenotypic legacy of admixture between modern humans and Neandertals

Simoniti C et al. Science Vol. 351, Issue 6274, pp. 737-741 (12 Feb 2016).

http://science.sciencemag.org/content/351/6274/737

5/3/16 Emily Kang (CCB) Paul Thomas

Emily Kang (CCB)

Phosphorylation of OPTN by TBK1 enhances its binding to Ub chains and promotes selective autophagy of damaged mitochondria

Richter B et al. PNAS vol. 113 no. 15 4039-4044 (2016).

http://www.pnas.org/content/113/15/4039.full

Paul Thomas

Endocytic sites mature by continuous bending and remodeling of the clathrin coat.

Avinoam et al. Science Vol. 348, Issue 6241, pp. 1369–72 (19 June 2015).

http://science.sciencemag.org/content/348/6241/1369.full

5/10/16 Emmalyn Chen Douglas Myers-Turnbull

Emmalyn Chen

Human Microbiota and Preterm Birth

Digiulio, D et al. PNAS Volume 112, p11060-65 (1 September 2015).

http://www.ncbi.nlm.nih.gov/pubmed/26283357

Douglas Myers-Turnbull

Neuro-immune Interactions Drive Tissue Programming in Intestinal Macrophages

Gabanyi I et al. Cell 164(3): 378-91 (2016 Jan 28).

http://www.ncbi.nlm.nih.gov/pubmed/26777404

5/17/16 Cole Helsell Michael Song

Cole Helsell

Ubiquitination independent of E1 and E2 enzymes by bacterial effectors

Qiu J. et al. Nature 533, no. 7601: 120–24 (May 5, 2016).

http://www.nature.com/nature/journal/v533/n7601/full/nature17657.html

Michael Song

DNA-based nanoparticle tension sensors reveal that T-cell receptors transmit defined pN forces to their antigens for enhanced fidelity

Liu Y et al. PNAS online (March 25, 2016).

http://www.pnas.org.ucsf.idm.oclc.org/content/early/2016/04/27/1600163113.full?sid=723959f4-6dfe-400f-8f8c-287adf7a2c76

5/24/16 David Bauer Fatima Ugur (CCB)

David Bauer

Genetic circuit design automation

Nielson, A et al. Science Vol. 352, Issue 6281 (1 April 2016).

http://science.sciencemag.org/content/352/6281/aac7341

Fatima Ugur (CCB)

Foldamer-mediated manipulation of a pre-amyloid toxin.

Kumar, S. et al. Nat. Commun. 2016, 7, 11412. (25 April 2016).

http://www.nature.com/ncomms/2016/160425/ncomms11412/full/ncomms11412.html

5/31/16 Charlotte Nelson Misha Vysotskly

Charlotte Nelson

Scaling in topological properties of brain networks

Singh S et al. Nature Scientific Reports 6, Article number: 24926 (2016).

http://www.nature.com/articles/srep24926

Misha Vysotskly

RNA splicing is a primary link between genetic variation and disease

Li Y.I. et al., Science Vol. 352, Issue 6285, pp. 600-604 (29 April 2016).

http://science.sciencemag.org/content/352/6285/600

6/7/16 Jasleen Sodhi

Jasleen Sodhi

Discovery of Novel Blood-Brian Barrier Targets to Enhance Brain Uptake of Therapeutic Antibodies

Zuchero YJ et al. Neuron 89(1):70-82 (2016 Jan 6).

6/14/16 Rim Hur Rachel Brunetti

Rim Hur

Hypothalamic control of male aggression-seeking behavior

Falkner et al, Nature Neuro Science Volume 19, Number 4 (April 2016).

http://www.nature.com/neuro/journal/v19/n4/full/nn.4264.html

Rachel Brunetti

Nuclear envelope rupture and repair during cancer cell migration

Denais, C. M. et al. Science, 352(6283), 353-358 (2016).

http://science.sciencemag.org/content/early/2016/03/23/science.aad7297

Academic YEAR 2015

Date Speaker 1 Speaker 2 Details
9/30/14 Orientation
10/7/14 Krister Barkovich (CCB) Ben Barad (Biophysics)

Krister Barkovich (CCB)

MTH1 inhibition eradicates cancer by preventing sanitation of the dNTP pool

Gad H et al., Nature (2014)

http://www.nature.com/nature/journal/v508/n7495/full/nature13181.html

Ben Barad (Biophysics)

Quantitative analysis of RNA-protein interactions on a massively parallel array reveals biophysical and evolutionary landscapes

Buenrostro J et al. Nature Biotechnology 32, 562–568 (2014).

http://www.nature.com/nbt/journal/v32/n6/full/nbt.2880.html

10/14/14 Nima Emami (Bioinformatics) Max Horlbeck (Biophysics)

Nima Emami (Bioinformatics)

A Probabilistic Model to Predict Clinical Phenotypic Traits from Genome Sequencing

Chen Y-C, Douville C, Wang C, Niknafs N, Yeo G, et al. (2014) A Probabilistic Model to Predict Clinical Phenotypic Traits from Genome Sequencing. PLoS Comput Biol 10(9): e1003825. doi: 10.1371/journal.pcbi.1003825

http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003825

Max Horlbeck (Biophysics)

Fringe proteins modulate Notch-ligand cis and trans interactions to specify signaling states

Lauren LeBon, Tom V Lee, Hamed Jafar-Nejad, David Sprinzak, Michael B Elowitz. eLife 2014;3:e02950

http://elifesciences.org/content/3/e02950

10/21/14 Zairan Liu (Biophysics) Geoff Smith (CCB)

Zairan Liu (Biophysics)

Stochastic but Highly Coordinated Protein Unfolding and Translocation by the ClpXP Proteolytic Machine

Cordova JC et al. Cell Volume 158, Issue 3, p647–658 (31 July 2014).

http://www.cell.com/abstract/S0092-8674%2814%2900800-9

Geoff Smith (CCB)

SMN2 splicing modifiers improve motor function and longevity in mice with spinal muscular atrophy.

Naryshkin, N.A. et al. Science 345, 688–693 (2014).

http://www.sciencemag.org/content/345/6197/688.figures-only

10/28/14 Jessica Friedman Justin Biel (Biophysics)

Jessica Friedman

Dystroglycan Binding to alpha-Neurexin Competes with Neurexophilin-1 and Neuroligin in the Brain

Reissner C et al. Journal of Biological Chemistry, Vol. 289, No. 40, pp. 27585-27603 (October 3, 2014).

http://www.jbc.org/content/289/40/27585.full.pdf+html

Justin Biel (Biophysics)

Understanding the catalytic efficiency of a model peroxiredoxin

Portillo-Ledesma S., et al. Biochemistry (2014) 53, 6113-6125

http://www.ncbi.nlm.nih.gov/pubmed/25184942

11/4/14 Joe Lobel (CCB) Lianne Pope (CCB)

Joe Lobel (CCB)

Mechanism of Activation of Protein Kinase JAK2 by the Growth Hormone Receptor

Brooks, AJ et al. Science (16 May 2014)

http://www.sciencemag.org/content/344/6185/1249783.abstract

Lianne Pope (CCB)

A molecular framework for temperature-dependent gating of ion channels

Chowdhury, et al. Cell 158 (5), 1148-1158 (2014).

http://www.cell.com/cell/abstract/S0092-8674(14)00976-3#

11/18/14 Clint Cario (Bioinformatics) Deanna Brackman

Clint Cario (Bioinformatics)

Precision microbiome reconstitution restores bile acid mediated resistance to Clostridium difficile

Buffie, Charlie G. et al. Nature doi:10.1038/nature13828 (22 October 2014)

http://www.nature.com/nature/journal/vaop/ncurrent/full/nature13828.html

Deanna Brackman

Artificial sweeteners induce glucose intolerance by altering gut microbiota

Suez J et al. Nature 514, 181–186 (09 October 2014).

http://www.nature.com/nature/journal/v514/n7521/full/nature13793.html

11/25/14 Sam Ivry Svetlana Lyalina (Bioinformatics)

Sam Ivry

Latency-Associated Degradation of the MRP1 Drug Transporter During Latent Human Cytomegalovirus Infection

Weekes MP et al. Science 340, 199 (2013); DOI: 10.1126/science.1235047

http://www.sciencemag.org/content/340/6129/199.short

Svetlana Lyalina (Bioinformatics)

Comparative analysis of regulatory information and circuits across distant species

Boyle AP et al. Nature (2014)

http://www.nature.com/nature/journal/v512/n7515/full/nature13668.html

12/2/14 Neville Bethel (Biophysics) Garrett Gaskins (Bioinformatics)

Neville Bethel (Biophysics)

Amplifying intracellular transport. Motion driven by stochastic, active forces.

Guo M. et al Cell 158, 822-832. August 14, 2014.

http://www.cell.com/abstract/S0092-8674%2814%2900924-6

Garrett Gaskins (Bioinformatics)

Life cycles, fitness decoupling and the evolution of multicellularity.

Hammerschmidt K et al. Nature 515, 75-79 (November 2014).

http://www.nature.com/nature/journal/v515/n7525/full/nature13884.html

1/6/15 Matt Ravalin (CCB) Angel Ku

Matt Ravalin (CCB)

Mind-controlled transgene expression by a wireless-powered optogenetic designer cell implant.

Folcher, M. et al. at. Commun. 5, 5392 (2014).

http://www.nature.com/ncomms/2014/141111/ncomms6392/full/ncomms6392.html

Angel Ku

Saturation editing of genomic regions by multiplex homology-directed repair

Findlay GM, et al. Nature 513, 120–123 (04 September 2014).

http://www.nature.com/nature/journal/v513/n7516/abs/nature13695.html

1/13/15 Samuel Thompson (Biophysics) Kojo Opoku-Nsiah (CCB)

Samuel Thompson (Biophysics)

Optical measurements of long-range protein vibrations.

Acbas G, et al., Nature Communications, 5:3076 (2014).

http://www.nature.com/ncomms/2014/140116/ncomms4076/full/ncomms4076.html

Kojo Opoku-Nsiah (CCB)

Opposing effects of folding and assembly chaperones on evolvability of Rubisco.

Durao P et al. Nat Chem Bio (2015)

http://www.nature.com/nchembio/journal/vaop/ncurrent/full/nchembio.1715.html

1/20/15 Alain Bonny (Biophysics) Joel Mefford

Alain Bonny (Biophysics)

Basal p21 controls population heterogeneity in cycling and quiescent cell cycle states

Overton, K.W. et al. (2014). Proc Natl Acad Sci USA 111(41):E4386-93

http://www.ncbi.nlm.nih.gov/pubmed/25267623

Joel Mefford

Scalable privacy-preserving data sharing methodology for genome-wide association studies

Yu F et al. J Biomed Inform. 2014 Aug;50:133-41.

http://www.ncbi.nlm.nih.gov/pubmed/24509073

1/27/15 Ilan Chemmama (Biophysics) Kevin Hartman (Bioinformatics)

Ilan Chemmama (Biophysics)

Sequential conformational rearrangements in flavivirus membrane fusion

Chao L et al. 5 December 2014 eLife 2014.

http://elifesciences.org/content/early/2014/12/05/eLife.04389

Kevin Hartman (Bioinformatics)

Convergent evolution and adaptation of Pseudomonas aeruginosa within patients with cystic fibrosis

Marvig R et al. Nature Genetics 47, 57–64 (2015).

http://www.nature.com/ng/journal/v47/n1/full/ng.3148.html

2/3/15 Allison Wong (CCB) Seth Axen (Bioinformatics)

Allison Wong (CCB)

A new antibiotic kills pathogens without detectable resistance

Ling L et al. Nature 517, 455–459 (22 January 2015).

http://www.nature.com/nature/journal/v517/n7535/full/nature14098.html

Seth Axen (Bioinformatics)

Time-resolved serial crystallography captures high-resolution intermediates of photoactive yellow protein

Tenboer J. et al. Science 5: Vol. 346 no. 6214 pp. 1242-1246 (December 2014).

http://www.sciencemag.org/cgi/doi/10.1126/science.1259357

2/10/15 Lillian Kenner (Biophysics) Hayley Donnella

Lillian Kenner (Biophysics)

Three-dimensional structure of human γ-secretase

Lu P et al. Nature 512, 166–170 (14 August 2014).

http://www.nature.com/nature/journal/v512/n7513/full/nature13567.html

Hayley Donnella

Multiplexed 3D cellular super-resolution imaging with DNA-PAINT and Exchange-PAINT

Jungmann R et al. Nat Methods. 2014 Mar;11(3):313-8.

http://www.nature.com/nmeth/journal/v11/n3/full/nmeth.2835.html

2/17/15 Megan Lo Chimno Nnadi (CCB)

Megan Lo

The Role of the Human Synaptic Vesicle Transporter SV2a

Madeo M et al. The Human Synaptic Vesicle Protein, SV2A, Functions as a Galactose Transporter in Saccharomyces cerevisiae. Journal of Biological Chemistry 289 (48): 33066-71 (Nov 28 2014).

http://www.ncbi.nlm.nih.gov/pubmed/25326386

Chimno Nnadi (CCB)

New Insights into Amyloid Beta Interactions with Human Telomerase

Wang et al JACS 2015.

http://pubs.acs.org/doi/abs/10.1021/ja511030s?journalCode=jacsat

2/24/15 Weilin Chen (Bioinformatics) Rachel Gate (Biophysics)

Weilin Chen (Bioinformatics)

Controlling low rates of cell differentiation through noise and ultrahigh feedback

Science Vol. 344 no. 6190 pp. 1384-1389 (20 June 2014).

http://www.sciencemag.org/content/344/6190/1384

Rachel Gate (Biophysics)

Genomic discovery of potent chromatin insulators for human gene therapy

Liu, et al. Nature Biotechnology. (2015)

http://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.3062.html

3/3/15 Bruk Mensa (CCB) Jasper Williams

Bruk Mensa (CCB)

Detecting Outer-membrane Stress by Monitoring β-barrel Assembly

Cho SH et al. "Detecting Envelope Stress by Monitoring β-Barrel Assembly". Cell (Dec 18, 2014).

http://www.ncbi.nlm.nih.gov/pubmed/25525882

Jasper Williams

Biopolymer implants enhance the efficacy of adoptive t-cell therapy

Stephan, SB et al. Biopolymer implants enhance the efficacy of adoptive t-cell therapy. Nature Biotechnology. 33, 97-101 (2015).

http://www.nature.com/nbt/journal/v33/n1/full/nbt.3104.html

3/31/15 Tyler Ross (Biophysics) Adolfo Cuesta (CCB)

Tyler Ross (Biophysics)

Interplay of Cell Shape and Division Orientation Promotes Robust Morphogenesis of Developing Epithelia

Xiong F et al. Cell 159 (2): 415-27 (2014 Oct 9).

http://www.ncbi.nlm.nih.gov/pubmed/25303534

Adolfo Cuesta (CCB)

Immunomodulatory lysophosphatidylserines are regulated by ABHD16A and ABHD12 interplay

Kamat S et al. Nat. Chem. Bio. 11, 171-164 (2015).

http://www.nature.com/nchembio/journal/v11/n2/full/nchembio.1721.html

4/7/15 Elena Caceras (Bioinformatics) Katherina Chua

Elena Caceras (Bioinformatics)

A Meta-Analysis Approach for Characterizing Pan-Cancer Mechanisms of Drug Sensitivity in Cell Lines

Wang K et al. PLOS One 9 (7): e103050 (18 July 2014).

http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0103050

Katherina Chua

Suppression of cancer relapse and metastasis by inhibiting cancer stemness

Li Y et al. PNAS, 112(6), 1839-1844 (February 10, 2015).

http://www.pnas.org/content/112/6/1839.short

4/14/15 Eugenia Salcedo (CCB) Evan Green (Biophysics)

Eugenia Salcedo (CCB)

Cationic lipid-mediated delivery of proteins enables efficient protein-based genome editing in vitro and in vivo

Zuris JA et al. Nature Biotechnology 33, 73–80 (January 2015).

http://www.nature.com/nbt/journal/v33/n1/full/nbt.3081.html

Evan Green (Biophysics)

Atomic Structure of T6SS Reveals Interlaced Array Essential to Function

Clemens, D et al. Cell, Volume 160, Issue 5, Pages 940–951 (26 February 2015).

http://www.cell.com/cell/abstract/S0092-8674%2815%2900138-5

4/21/15 Leanna Morinishi (Biophysics)

Leanna Morinishi (Biophysics)

Spatial reconstruction of single-cell gene expression data

Satija, R et al. Nature Biotechnology. 13 April 2015.

http://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.3192.html

4/28/15 Steven Moss (CCB) Stefan Niekamp (Biophysics)

Steven Moss (CCB)

De novo biosynthesis of terminal alkyne-labeled natural products

Zhu, X.; Liu, J.; Zhang, W. Nature Chemical Biology 11, 115-120 (2015).

http://www.nature.com/nchembio/journal/v11/n2/full/nchembio.1718.html

Stefan Niekamp (Biophysics)

Trajectories of the ribosome as a Brownian nanomachine

Dashti A et al. PNAS Vol 111 no. 49, 17492–17497 (December 9, 2014).

http://www.pnas.org/content/111/49/17492.full.pdf+html

5/5/15 Meena Subramaniam (Bioinformatics) Kaitlin Hulce (CCB)

Meena Subramaniam (Bioinformatics)

Sensitive detection of chromatin-altering polymorphisms reveals autoimmune disease mechanisms

Del Rosario, R. C.-H. et al. Nat. Methods (23 March 2015).

http://www.nature.com/nmeth/journal/vaop/ncurrent/full/nmeth.3326.html

Kaitlin Hulce (CCB)

Targeting diverse protein-protein interaction interfaces with a/b-peptides derived from the Z-domain scaffold.

Checco JW et al. Proc. Natl. Acad. Sci. USA. 2015, 112, 4552.

http://www.pnas.org/content/112/15/4552.full.pdf

5/12/15 Darya Cheng Eugene Palovcak (Biophysics)

Darya Cheng

RBM3 mediates structural plasticity and protective effects of cooling in neurodegeneration

Peretti D et al. Nature 518, 236–239 (12 February 2015).

http://www.nature.com/nature/journal/v518/n7538/full/nature14142.html

Eugene Palovcak (Biophysics)

A molecular census of 26S proteasomes in intact neurons

Asano S et al. Science 23 January 2015: 347 (6220), 439-442.

http://www.sciencemag.org/content/347/6220/439.abstract

5/19/15 Ryan Muir (CCB) Reed Stein

Ryan Muir (CCB)

A semi-synthetic organism with an expanded genetic alphabet.

Malyshev D et al. Nature 509, 385–388 (15 May 2014).

http://www.nature.com/nature/journal/v509/n7500/full/nature13314.html

Reed Stein

Preventing proteostasis diseases by selective inhibition of a phosphatase regulatory subunit

Das I et al. Science Vol. 348 no. 6231 pp. 239-242 (10 April 2015)

http://www.sciencemag.org/content/348/6231/239.abstract

5/26/15 Marco Mravic Stephanie See (CCB)

Stephanie See (CCB)

Intercellular chaperone transmission via exosomes contributes to maintenance of protein homeostasis at the organismal level

Takeuchi T et al. PNAS Early Edition p. 1-10 (24 March 2015).

6/2/15 Jessica Enogieru Erin Poss (CCB)

Jessica Enogieru

Elucidating Molecular Phenotypes caused by the SORL1 Alzheimer's Disease Genetic Risk Factor Using Human Induced Pluripotent Stem cells

Young JE et al. Cell Stem Cell. 2015 Apr 2;16(4):373-85 (2015 Mar 12).

http://www.sciencedirect.com/science/article/pii/S1934590915000600

Erin Poss (CCB)

MEK guards proteome stability and inhibits tumor-suppressive amyloidogenesis via HSF1.

Tang Z et al. Cell. 160 (4): 729 -44. (Feb 12 2015).

http://www.ncbi.nlm.nih.gov/pubmed/25679764

6/9/15 Christine Bowman Weiyue Ji (Biophysics)

Christine Bowman

An implantable microdevice to perform high-throughput in vivo drug sensitivity testing in tumors

Jonas O et al. Sci. Transl. Med Vol. 7, Issue 284, p. 284ra57 (22 April 2015).

http://stm.sciencemag.org/content/7/284/284ra57.full

Weiyue Ji (Biophysics)

MicroRNA control of protein expression noise

Rizvi N.A. et al. (2015). Science 348, 124–128.

http://www.ncbi.nlm.nih.gov/pubmed/25838385

Academic YEAR 2014

Date Speaker 1 Speaker 2 Details
10/1/13 Orientation
10/8/13 Christina Homer (Biophysics) Rob Weber (CCB)

Christina Homer (Biophysics)

Salmonella typhimurium intercepts Escherichia coli signaling to enhance antibiotic tolerance

Vega NM, Allision KR, Samuels AN, Klempner MS, and Collins JJ. 2013. PNAS (110:35), 14420-14425.

http://www.ncbi.nlm.nih.gov/pubmed/23946425

Rob Weber (CCB)

Self-assembling influenza nanoparticle vaccines elicit broadly neutralizing H1N1 antibodies

Kanekiyo M. et al. Nature 499, 102-106 (04 July 2013).

http://www.nature.com/nature/journal/v499/n7456/full/nature12202.html

10/15/13 Alex Martinko (CCB) Andrew Sczesnak (Bioinformatics)

Alex Martinko (CCB)

Temporal regulation of EGF signalling networks by the scaffold protein Shc1

Zheng, Y. et al. Nature 499, 166–171 (11 July 2013).

http://www.nature.com/nature/journal/v499/n7457/full/nature12308.html#ref32

Andrew Sczesnak (Bioinformatics)

Out-of-Africa migration and Neolithic coexpansion of Mycobacterium tuberculosis with modern humans.

Comas I et al. Nat Genet. 2013 Oct;45(10):1176-82. doi: 10.1038/ng.2744.

http://www.ncbi.nlm.nih.gov/pubmed/23995134

10/22/13 Miguel Betegon (Biophysics) Kyle Defrees (CCB)

Miguel Betegon (Biophysics)

Gut Microbiota from Twins Discordant for Obesity Modulate Metabolism in Mice

Ridaura, VK et al. Science 6 September 2013: Vol. 341 no. 6150.

http://www.sciencemag.org/content/341/6150/1241214

Kyle Defrees (CCB)

Small-molecule antagonists of melanopsin-mediated phototransduction

Jones, Kenneth A. et al. Nature Chemical Biology 9, 630-635 (2013).

http://www.nature.com/nchembio/journal/v9/n10/full/nchembio.1333.html

10/29/13 Jennifer Kung (CCB) Veronica Pessino (Biophysics)

Jennifer Kung (CCB)

Structural Rearrangement of Ebola Virus VP40 Begets Multiple Functions in the Virus Life Cycle.

Bornholdt, Z. A. et al. Cell 154, 763–774 (2013).

http://www.cell.com/abstract/S0092-8674(13)00886-6

Veronica Pessino (Biophysics)

Defining Single Molecular Forces Required to Activate Integrin and Notch Signaling

Xuefeng Wang and Taekjip Ha Science 340, 991 (2013).

http://www.sciencemag.org/content/340/6135/991.full

11/5/13 Leo Gendelev (Biophysics) Kieran Mace (Bioinformatics)

Leo Gendelev (Biophysics)

Modulation of allostery by protein intrinsic disorder

Ferreon et al, Nature 498, 390–394 (20 June 2013).

http://www.nature.com/nature/journal/v498/n7454/full/nature12294.html

Kieran Mace (Bioinformatics)

Slower recovery in space before collapse of connected populations

Dai, L et al. Nature 496, 355–358 (18 April 2013).

http://www.nature.com/nature/journal/v496/n7445/full/nature12071.html

11/12/13 Daniel Gentile (CCB) John Hawkins (Biophysics)

Daniel Gentile (CCB)

Odour receptors and neurons for DEET and new insect repellents

Kain, P. et al. Nature online 02 October 2013.

http://www.nature.com/nature/journal/vaop/ncurrent/full/nature12594.html

John Hawkins (Biophysics)

Notch Inhibition Induces Cochlear Hair Cell Regeneration and Recovery of Hearing after Acoustic Trauma

Mizutari, K. et al. Neuron, Volume 78, Issue 2, 24 April 2013, Page 403.

http://www.sciencedirect.com/science/article/pii/S0896627312009531#

11/19/13 Brian O'Donovan (Bioinformatics) Brian Sharon (Biophysics)

Brian O'Donovan (Bioinformatics)

Genomically Recoded Organisms Expand Biological Functions

Lajoie, M. et al. Science 18 October 2013: Vol. 342 no. 6156 pp. 357-360.

http://www.sciencemag.org/content/342/6156/357

Brian Sharon (Biophysics)

Rate of environmental change determines stress response specificity.

Young, JW et al. PNAS. 2013 Mar 5;110(10):4140-5. doi: 10.1073/pnas.1213060110.

http://www.ncbi.nlm.nih.gov/pubmed/23407164

11/26/13 Isabelle Taylor (CCB) Jordi Silvestre-Ryan (Biophysics)

Isabelle Taylor (CCB)

Targeting isoprenylcysteine methylation ameliorates disease in a mouse model of progeria.

Ibrahim, M.X. et al. (2013). Science, 340: 1330-1333.

http://www.sciencemag.org/content/340/6138/1330.long

Jordi Silvestre-Ryan (Biophysics)

Long-Term Dynamics of Adaptation in Asexual Populations

Wiser, M.J. et al. Science 2013 (early edition, online only).

http://twileshare.com/uploads/Science-2013-Wiser-science.1243357_.pdf

12/3/13 Amanda Loshbaugh (Biophysics) Rebecca Freilich (CCB)

Amanda Loshbaugh (Biophysics)

Positive feedback between PU.1 and the cell cycle controls myeloid differentiation

Kueh, H.Y. et al. Science Vol 341 pp 670-673 (2013).

http://www.sciencemag.org/content/341/6146/670.abstract

Rebecca Freilich (CCB)

A Zebrafish Embryo Culture System Defines Factors that Promote Vertebrate Myogenesis across Species

Xu, C. et al. Cell Vol. 155 Issue 4 pp. 909-921 (7 November 2013)

http://www.cell.com/abstract/S0092-8674%2813%2901299-3

1/7/14 Sam Pollock (CCB) Rebecca Davidson (Biophysics)

Sam Pollock (CCB)

Functional lysine modification by an intrinsically reactive primary glycolytic metabolite.

Moellering, R. E., & Cravatt, B. F. (2013). Science (New York, N.Y.), 341(6145), 549–553. doi:10.1126/science.1238327

http://www.sciencemag.org/content/341/6145/549.full

Rebecca Davidson (Biophysics)

What makes a protein fold amenable to functional innovation? Fold polarity and stability trade-offs.

Dellus-Gur, E. et al. What makes a protein fold amenable to functional innovation? Fold polarity and stability trade-offs. J Mol Biol. Vol. 245 Issue 14 pp. 2609-21 (24 July 2013).

http://www.ncbi.nlm.nih.gov/pubmed/23542341

1/14/14 Pradeep Bandaru (Biophysics) Yuan Gao (Biophysics)

Pradeep Bandaru (Biophysics)

Nonenzymatic Template-Directed RNA Synthesis Inside Model Protocells

Katarzyna, A. et al. Science 342, 1098 (2013).

http://molbio.mgh.harvard.edu/szostakweb/publications/Szostak_pdfs/Adamala_Szostak_2013_Science.pdf

Yuan Gao (Biophysics)

Voltage-Gated Sodium Channel in Grasshopper Mice Defends Against Bark Scorpion Toxin

Rowe, A.H. et al. Science Vol. 342 no. 6157 pp. 441-446 (25 October 2013).

http://www.sciencemag.org/content/342/6157/441

1/21/14 Ted Ho (Biophysics) Zygy Roe-Zurz (Biophysics)

Ted Ho (Biophysics)

Sirt1 Extends Life Span and Delays Aging in Mice through the Regulation of Nk2 Homeobox 1 in the DMH and LH

Satoh, Akiko, et al. Cell metabolism18.3 (2013): 416-430.

http://www.cell.com/cell-metabolism/abstract/S1550-4131%2813%2900333-1

Zygy Roe-Zurz (Biophysics)

Constraining Exoplanet Mass from Transmission Spectroscopy

Wit, J et al. Science Vol. 342, pp. 1473-1477 (2013).

http://m.sciencemag.org/content/342/6165/1473.full.pdf

1/28/14 Geoff Smith (CCB)

Geoff Smith (CCB)

Brd4 and JMJD6-Associated Anti-Pause Enhancers in Regulation of Transcriptional Pause Release.

Liu, W., et al. Brd4 and JMJD6-Associated Anti-Pause Enhancers in Regulation of Transcriptional Pause Release. Cell 155, 1581–1595 (2013).

http://www.cell.com/abstract/S0092-8674%2813%2901474-8

2/4/14 Krister Barkovich (CCB) Benjamin Barad (Biophysics)

Krister Barkovich (CCB)

Activation Loop Dynamics Determine the Different Catalytic Efficiencies of B Cell- and T Cell-Specific Tec Kinases

Joseph RE et al. Science Signaling 2013 Aug 27; 6(290).

http://stke.sciencemag.org/cgi/content/full/sigtrans;6/290/ra76/DC1

Benjamin Barad (Biophysics)

Three-dimensional electron crystallography of protein microcrystals

Shi, D. et al. eLife 2, (Nov 2013).

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3831942/

2/11/14 Neville Bethel (Biophysics) Zairan Liu (Bioinformatics)

Neville Bethel (Biophysics)

Cytoplasmic Volume Modulates Spindle Size During Embryogenesis

Matthew C. Good, Michael D. Vahey, Arunan Skandarajah, Daniel A. Fletcher, Rebecca Heald Science 342, 856 (2013); DOI: 10.1126/science.1243147

https://www.sciencemag.org/content/342/6160/856.abstract

Zairan Liu (Bioinformatics)

Where to go? Back seat driver taking control!

Dona, E. et al. Directional tissue migration through a self-generated chemokine gradient. Nature (2013) Published online 25 September 2013.

http://www.nature.com/nature/journal/vaop/ncurrent/full/nature12635.html

2/18/14 Svetlana Lyalina (Biophysics) Ilan Chemmama (Biophysics)

Svetlana Lyalina (Biophysics)

Genome-wide comparison of medieval and modern Mycobacterium leprae.

Schuenemann, V. J. et al. Science 341, 179–183 (2013).

https://www.sciencemag.org/content/341/6142/179.abstract

Ilan Chemmama (Biophysics)

Dengue virus envelope protein domain I/II hinge determines long-lived serotype-specific dengue immunity

Messer, WB et al. PNAS, published ahead of print January 2, 2014.

http://www.pnas.org/content/early/2014/01/02/1317350111.abstract

2/25/14 Joseph Lobel (CCB) Alain Bonny (Biophysics)

Joseph Lobel (CCB)

Antidiabetic effects of glucokinase regulatory protein small-molecule disruptors

Lloyd, DJ. et al. Nature. 2013 Dec 19;504(7480):437-40

http://www.nature.com/nature/journal/vaop/ncurrent/full/nature12724.html

Alain Bonny (Biophysics)

The ClpXP Protease Unfolds Substrates Using a Constant Rate of Pulling but Different Gears.

Sen, M. et al. Cell 155, 636-646 (2013).

https://www.cell.com/abstract/S0092-8674%2813%2901159-8

3/4/14 Justin Biel (Biophysics) Clinton Cario (Bioinformatics)

Justin Biel (Biophysics)

Unnatural DNA base pairs with Watson-Crick geometry: Expanding the genetic code

Betz K, et al. Structural Insights into DNA Replication without Hydrogen Bonds. J Am Chem Soc. 2013 Dec 11;135(49):18637-43. doi: 10.1021/ja409609j. Epub 2013 Nov 27

http://pubs.acs.org/doi/abs/10.1021/ja409609j

Clinton Cario (Bioinformatics)

Cancer Ecology and Evolution

Bolli, N et al. Heterogeneity of genomic evolution and mutational profiles in multiple myeloma. Nat Commun. 2014 Jan 16;5:2997

http://www.nature.com/ncomms/2014/140116/ncomms3997/full/ncomms3997.html

3/11/14 Samuel Thompson (Biophysics) Kevin Hartman (Bioinformatics)

Samuel Thompson (Biophysics)

Nanoscale imaging reveals laterally expanding antimicrobial pores in lipid bilayers

Rakowska, P.D. et al. PNAS Vol. 110 No. 22, pp. 8918-8923 (May 28, 2013).

http://www.pnas.org/content/110/22/8918

Kevin Hartman (Bioinformatics)

In vitro selection with artificial expanded genetic information systems

Sefah, K et al. (November 19, 2013) PNAS

3/25/14 Matthew Ravalin (CCB) Nima Emami (Bioinformatics)

Matthew Ravalin (CCB)

The siderophore yersiniabactin binds copper to protect pathogens during infection.

Chaturvedi, K. S. et al. Nat. Chem. Biol. 8, 731–6 (2012).

http://www.ncbi.nlm.nih.gov/pubmed/22772152

Nima Emami (Bioinformatics)

A prostate cancer susceptibility allele at 6q22 increases RFX6 expression by modulating HOXB13 chromatin binding

Huang, Q et al. Nature Genetics 46, 126–135 (2014).

http://www.nature.com/ng/journal/v46/n2/full/ng.2862.html

4/1/14 Max Horlbeck (Bioinformatics) Kwadwo Opoku-Nsiah (CCB)

Max Horlbeck (Bioinformatics)

Conformation capture of the mitotic chromosome

Naumova, N. et al. Science, November 22, 2013.

https://www.sciencemag.org/content/342/6161/948?related-urls=yes&legid=sci;342/6161/948

Kwadwo Opoku-Nsiah (CCB)

Microbiota modulate behavioral and physiological abnormalities associated with neurodevelopmental disorders

Hsiao EY, et al. Cell. 155, 1451-1463 (2013).

http://www.cell.com/abstract/S0092-8674%2813%2901473-6

4/8/14 Lianne Devera (CCB) Garrett Gaskins (Biophysics)

Lianne Devera (CCB)

Targeting a Dual Detector of Skin and CO2 to Modify Mosquito Host Seeking

Tauxe, G. M. et al. 2013. Cell. 155: 1365-1379. December 5th, 2013.

http://www.cell.com/abstract/S0092-8674%2813%2901426-8

Garrett Gaskins (Biophysics)

Potential Vulnerabilities in ChIP-Seq data.

Teytelman et al., (2013) Highly expressed loci are vulnerable to misleading ChIP localization of multiple unrelated proteins. Proc Natl Acad Sci USA 110:18602-7; doi 10.1073/pnas.1316064110

http://www.ncbi.nlm.nih.gov/pubmed/24173036

Academic YEAR 2013

Date Speaker 1 Speaker 2 Details
9/25/12 Orientation
10/2/12 Kyle Barlow Noah Younger

Kyle Barlow

Schaub, M. A., Boyle, A. P., Kundaje, A., Batzoglou, S. & Snyder, M. Linking disease associations with regulatory information in the human genome. Genome Res. 22, 1748–1759 (2012).

Noah Younger

Illing PT et al. Immune self-reactivity triggered by drug-modified HLA-peptide repertoire. Nature. 2012; 486:554-558.

10/9/12 Thomas Stevens Marian Deuker

Thomas Stevens

Santos, Silvia D M et al. Spatial Positive Feedback at the Onset of Mitosis. Cell 149.7 (2012): 1500-13.

Marian Deuker

http://www.cell.com/abstract/S0092-8674%2812%2900643-5

10/16/12 Amy Jacobson Andrew VanBenschoten

Amy Jacobson

Khare, S.D., et al. Computational redesign of a mononuclear zinc metalloenzyme for organophosphate hydrolysis. Nat. Chem. Biol. 8, 294-300 (2012).

Andrew VanBenschoten

Allosteric control of the ribosome by small-molecule antibiotics" (Wang L et.al, Nature Structural & Molecular Biology (2012) 19:9 957-963).

10/23/12 John Haliburton Jordan Carelli

John Haliburton

Gene location and DNA density determine transcription factor distributions in Escherichia coli. Thomas E Kuhlman and Edward C Cox. Molecular Systems Biology 8; Article number 610; doi:10.1038/msb2012.42

Jordan Carelli

Systems-pharmacology dissection of a drug synergy in imatinib-resistant CML", which was published in Nature Chemical Biology on 30 September, 2012

10/30/12 Ben Heineike Kale Kundert

Ben Heineike

1: Thurman RE, et al. The accessible chromatin landscape of the human genome. Nature. 2012 Sep 6;489(7414):75-82. doi: 10.1038/nature11232. PubMed PMID: 22955617.

Kale Kundert

Shiou Tzeng and Charalampos Kalodimos. Protein activity regulation by conformational entropy. August 2012. Nature 488:236-240

11/6/12 Greg Fedewa Louise Goupil

Greg Fedewa

Evidence that viral RNAs have evolved for efficient, two-stage packaging. PNAS (2012) vol 109 no. 39

Louise Goupil

Direct identification of ligand-receptor interactions on living cells and tissues". Frei et al. Nature Biotechnol. 2012 Sep 16. doi: 10.1038/nbt.2354

11/13/12 Amy Chang Daniel Himmelstein

Amy Chang

A logic-gated nanorobot for targeted transport of molecular payloads. SM Douglas, I Bachelet, GM Church (2012) Science. 335:831–4

Daniel Himmelstein

Chris R. Reid, Tanya Lattya, Audrey Dussutour, and Madeleine Beekman. Slime mold uses an externalized spatial “memory” to navigate in complex environments. PNAS October 23, 2012 vol. 109 no. 43 17490-17494

11/20/12 Ben Spangler Peter Fellowes

Ben Spangler

A magnetic switch for the control of cell death signalling in in vitro and in vivo systems, Mi Hyeon Cho, et. al. http://www.nature.com/nmat/journal/vaop/ncurrent/pdf/nmat3430.pdf

Peter Fellowes

Substitutions in woolly mammoth hemoglobin confer biochemical properties adaptive for cold tolerance" (Nature Genetics, 2010)

11/27/12 Nicole Olson Jack Yue

Nicole Olson

Antibiotics in early life alter the murine colonic microbiome and adiposity. Nature, 488, pp. 621–626 (30 August 2012).

Jack Yue

Injectable preformed scaffolds with shape-memory properties. PNAS October 16th, 2012 by Bencherif et al.

12/4/12 Kay Aull Tara Friedrich

Kay Aull

Originally published in Science Express on October 18 2012 Science 23 November 2012: vol. 338 no. 6110 pp. 1076-1080 Structural Basis of Transcription Initiation Yu Zhang, Yu Feng, Sujoy Chatterjee, Steve Tuske, Mary X. Ho, Eddy Arnold, Richard H. Ebright

Tara Friedrich

Waves of Retrotransposon Expansion Remodel Genome Organization and CTCF Binding in Multiple Mammalian Lineages Schmidt D, et. al. Cell, Volume 148, Issue 1, 335-348, 12 January 2012

1/8/13 Alex Pankov Kate Southard

Alex Pankov

The Geometric Structure of the Brain Fiber Pathways (http://www.sciencemag.org/content/335/6076/1628.abstract).

Kate Southard

Synthetic two way communication between mamelian cells. http://www.nature.com/nbt/journal/v30/n10/full/nbt.2351.html

1/15/13 Juan Perez Bermejo Diego Garrido Ruiz

Juan Perez Bermejo

K. Hayashi, H. Ohta, K. Kurimoto, S. Aramaki, M. Saitou. Reconstitution of the mouse germ cell specification pathway in culture by pluripotent stem cells. Cell, 146 (2011), pp. 519–532

Diego Garrido Ruiz

Cancer resistance in the blind mole rat is mediated by concerted necrotic cell death mechanism Vera Gorbunova, Christopher Hine, Xiao Tian, Julia Ablaeva, Andrei V. Gudkov, Eviatar Nevo, andAndrei Seluanov. PNAS November 20, 2012 vol. 109 no. 47 19392-19396

1/22/13 Patrick Harrigan Weihan Li

Patrick Harrigan

Scaling of embryonic patterning based on phase-gradient encoding http://www.ncbi.nlm.nih.gov/pubmed/23254931

Weihan Li

Stochastic Pulse Regulation in Bacterial Stress Response Science, 2011, 334, 366–369.

1/29/13 David Mavor Stephen Nayfach

David Mavor

Visualizing transient low-populated structures of RNA

http://www.nature.com/nature/journal/v491/n7426/full/nature11498.html

Stephen Nayfach

Genomic variation landscape of the human gut microbiome

http://www.nature.com/nature/journal/v493/n7430/full/nature11711.html

2/5/13 Naomi Yonis (CCB) Robert Schiemann (Bioinformatics)

Naomi Yonis (CCB)

DNA-repair scaffolds dampen checkpoint signalling by counteracting the adapter Rad9 http://www.nature.com/nature/journal/v493/n7430/full/nature11658.html

Robert Schiemann (Bioinformatics)

A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity.

Jinek, M., Chylinski, K., Fonfara, I., Hauer, M., Doudna, J. a, & Charpentier, E. Science. 2012 17 Aug; 337(6096), 816-21.

2/12/13 Rose Citron (Biophysics) Christina Fitzsimmons (CCB)

Rose Citron (Biophysics)

p53 Dynamics Control Cell Fate

Jeremy E. Purvis et al. Science, Vol 336, 1440-4 (15 June 2012)

Christina Fitzsimmons (CCB)

Community surveillance enhances Pseudomonas aeruginosa virulence during polymicrobial infection.

Korgaonkar et al. PNAS 2013, 110 (3), 1059-1064.

2/19/13 Justin Meyerowitz (CCB) Russell Goodman (Biophysics)

Justin Meyerowitz (CCB)

Regulation of mTORC1 by the Rag GTPases is necessary for neonatal autophagy and survival

Efeyan et al., Nature, 2013.

http://www.nature.com/nature/journal/v493/n7434/full/nature11745.html

Russell Goodman (Biophysics)

Structural basis for selective activation of ABA receptors.

Peterson FC, Burgie ES, Park S, Jensen DR, Weiner JJ, Bingman CA, Chang CA, Cutler SR, Phillips GN, Volkman BF. Nat. Struct. Mol. Biol. 17,1109-1114 (2010).

2/26/13 Rebecca Levin (CCB) Graham Heimberg (Bioinformatics)

Rebecca Levin (CCB)

Variable Clonal Repopulation Dynamics Influence Chemotherapy Response in Colorectal Cancer.

Kreso, A. et al. Science (New York, N.Y.) 543, (2012).

Graham Heimberg (Bioinformatics)

1. Next-Generation Digital Information Storage in DNA 2. Towards practical, high-capacity, low-maintenance information storage in synthesized DNA

1. George M. Church, Yuan Gao, Sriram Kosuri 28 SEPTEMBER 2012 VOL 337 SCIENCE 2.Nick Goldman, Paul Bertone, Siyuan Chen, Christophe Dessimoz, Emily M. LeProust, Botond Sipos & Ewan Birney January 23, Nature, 2013

3/5/13 Sara Calhoun (Biophysics) Rahel Woldeyes (CCB)

Sara Calhoun (Biophysics)

A Whole-Cell Computational Model Predicts Phenotype from Genotype.

JR Karr, JC Sanghvi, DN Macklin, MV Gutschow, JM Jacobs, B Bolival, Jr., N Assad-Garcia, JI Glass, and MW Covert (2012) Cell, 150, 389-401.

Rahel Woldeyes (CCB)

Explaining why gleevec is a specific and potent inhibitor of abl kinase.

Lin, Y. L., Meng, Y., Jiang, W., & Roux, B. (2013). Proceedings of the National Academy of Sciences of the United States of America, 110(5), 1664-1669.

3/12/13 Sarah Woldemariam (CCB) James Webber (Bioinformatics)

Sarah Woldemariam (CCB)

Tuning the Electronic Absorption of Protein-Embedded All-trans-Retinal

Wang, et al. Tuning the Electronic Absorption of Protein-Embedded All-trans-Retinal (2012) Science Vol 338, 1340-1343.

James Webber (Bioinformatics)

Minimal "Self" Peptides That Inhibit Phagocytic Clearance and Enhance Delivery of Nanoparticles Pia L. Rodriguez, Takamasa Harada, David A. Christian, Diego A. Pantano, Richard K. Tsai, Dennis E. Discher Science 22 February 2013

3/26/13 Rebecca Davidson (Biophysics) Miguel Betegon (Bioinformatics)

Rebecca Davidson (Biophysics)

Pheromonal and behavioral cues trigger male-to-female aggression in Drosophila

http://www.ncbi.nlm.nih.gov/pubmed/21124886

Miguel Betegon (Bioinformatics)

A bacteriophage encodes its own CRISPR/Cas adaptive response to evade host innate immunity.

Seed, K. D., Lazinski, D. W., Calderwood, S. B., & Camilli, A. Nature, 494(7438), 489-491. doi:10.1038/nature11927 (2013)

4/2/13 Christina Homer (Biophysics) Rob Weber (CCB)

Christina Homer (Biophysics)

Integration of Chemical and RNAi Multiparametric Profiles Identifies Triggers of Intracellular Mycobacterial Killing.

Cell Host Microbe. 2013 Feb 13;13(2):129-42. doi: 10.1016/j.chom.2013.01.008.

http://www.ncbi.nlm.nih.gov/pubmed/23414754

Rob Weber (CCB)

Selective Protein Synthesis by Ribosomes with a Drug-Obstructed Exit Tunnel.

Krishna Kannan, Nora Vázquez-Laslop, Alexander S. Mankin. Cell, Volume 151, Issue 3, 508-520, 26 October 2012.

http://www.ncbi.nlm.nih.gov/pubmed/23101624

4/9/13 Rebecca Freilich (CCB) Andrew Sczesnak (Bioinformatics)

Rebecca Freilich (CCB)

High Salt Recruits Aversive Taste Pathways.

Yuki Oka, Matthew Butnaru, Lars von Buchholtz, Nicholas J.P. Rybe and Charles Zuker. Nature, Volume 494, Issue 28, 472-475, 28 February 2013.

http://www.ncbi.nlm.nih.gov/pubmed/23407495

Andrew Sczesnak (Bioinformatics)

Host-derived nitrate boosts growth of E. coli in the inflamed gut.

Science. 2013 Feb 8;339(6120):708-11. doi: 10.1126/science.1232467.

http://www.ncbi.nlm.nih.gov/pubmed/23393266

4/16/13 Amanda Loshbaugh (Biophysics) Pradeep Bandaru (Bioinformatics)

Amanda Loshbaugh (Biophysics)

Mesenchymal stem cell-based cell engineering with multifunctional mesoporous silica nanoparticles for tumor delivery

Huang X. et al. Biomaterials Volume 34, Issue 7, February 2013, Pages 1772 - 1780.

http://www.sciencedirect.com/science/article/pii/S0142961212012914

Pradeep Bandaru (Bioinformatics)

Beyond Secondary Structure: Primary-Sequence Determinants License Pri-miRNA Hairpins for Processing

Auyeung V.C. et al. Cell Volume 152, Issue 4, 14 February 2013, Pages 844 - 858.

http://www.sciencedirect.com/science/article/pii/S0092867413000834

4/23/13 John Hawkins (Biophysics) Brian O'Donovan (Bioinformatics)

John Hawkins (Biophysics)

General protein diffusion barriers create compartments within bacterial cells.

Schlimpert S et al. Cell. 2012 Dec 7;151(6):1270-82. doi: 10.1016/j.cell.2012.10.046. Epub 2012 Nov 29.

http://www.ncbi.nlm.nih.gov/pubmed/23201141

Brian O'Donovan (Bioinformatics)

A Guanosine-Centric Mechanism for RNA Chaperone Function

Grohman J. K. et al. Science 12 April 2013: Vol. 340 no. 6129 pp. 190-195.

http://www.sciencemag.org/content/340/6129/190.full

4/30/13 Alex Martinko (CCB) Veronica Pessino (Biophysics)

Alex Martinko (CCB)

Quantitative analysis of HSP90-client interactions reveals principles of substrate recognition.

Taipale, M. et al. Cell 150, 987 - 1001 (2012).

http://www.ncbi.nlm.nih.gov/pubmed/22939624

Veronica Pessino (Biophysics)

Loss of electrostatic cell-surface repulsion mediates myelin membrane adhesion and compaction in the central nervous system.

Bakhti M et al. Proc Natl Acad Sci U S A. 2013 Feb 19;110(8):3143-8. doi: 10.1073/pnas.1220104110. Epub 2013 Feb 4.

http://www.ncbi.nlm.nih.gov/pubmed/23382229

5/7/13 Kieran Mace (Bioinformatics) Jennifer Kung (CCB)

Kieran Mace (Bioinformatics)

Evolutionary trade-offs, Pareto optimality, and the geometry of phenotype space.

Shoval, O. et al. Science 336, 1157-1160 (2012).

https://www.sciencemag.org/content/339/6121/757.3.abstract

Jennifer Kung (CCB)

Mechanism-Based Covalent Neuraminidase Inhibitors with Broad Spectrum Influenza Antiviral Activity

Kim, JH. et al. Science 340, 71 (2013).

http://www.sciencemag.org/content/340/6128/71.full

5/14/13 Sam Pollock (CCB) Leo Gendelev (Biophysics)

Sam Pollock (CCB)

Chronic Stress Triggers Social Aversion via Glucocorticoid Receptor in Dopaminoceptive Neurons

Bark, J. et al. Science 18 January 2013: Vol. 339 no. 6117 pp. 332-335 .

http://www.sciencemag.org/content/339/6117/332.full

Leo Gendelev (Biophysics)

Protein Complexes Are under Evolutionary Selection to Assemble via Ordered Pathways

Marsh, J.A. et al. Cell, Volume 153, Issue 2, 461-470, 11 April 2013.

http://www.sciencedirect.com/science/article/pii/S009286741300278X

5/21/13 Daniel Gentile (CCB)

Daniel Gentile (CCB)

Photochemical Activation of TRPA1 Channels in Neurons and Animals.

Kokel, D et al. Nature Chemical Biology 9, 257-263 (2013).

http://www.nature.com/nchembio/journal/v9/n4/full/nchembio.1183.html

5/28/13 Zygy Roe-Zurz (Biophysics) Isabelle Taylor (CCB)

Zygy Roe-Zurz (Biophysics)

Zhijian Chen's initial discovery of cyclic dinucleotides in metazoa Zhijian Chen's near immediate follow up in the discovery of the responsible cyclase Tom Tuschl's structure of cGAS that revises the connectivity of the cyclic dinucleotide

http://www.sciencemag.org/content/339/6121/826.abstract, http://www.sciencemag.org/content/339/6121/786.abstract, http://www.cell.com/abstract/S0092-8674(13)00522-9

Isabelle Taylor (CCB)

Biomimetic enzyme nanocomplexes and their use as antidotes and preventive measures for alcohol intoxication

Liu, Y. et al., Nature Nanotechnology 8, 187-192 (2013).

http://www.nature.com/nnano/journal/v8/n3/full/nnano.2012.264.html

6/4/13 Jordi Silvestre-Ryan (Biophysics) Kyle DeFrees (CCB)

Jordi Silvestre-Ryan (Biophysics)

Synthetic analog computation in living cells

Daniel, R. et al, Nature 15 May 2013. Online.

http://www.nature.com/nature/journal/vaop/ncurrent/full/nature12148.html

Kyle DeFrees (CCB)

DAGLB inhibition perturbs a lipid network involved in macrophage inflammatory responses

Hsu, Ku-Lung et al., Nature Chemical Biology 8, 999-1007 (2012).

http://www.nature.com/nchembio/journal/v8/n12/full/nchembio.1105.html

6/11/13 Yuan Gao (Biophysics) Ted Ho (Biophysics)

Yuan Gao (Biophysics)

mTOR Regulates Lysosomal ATP-Sensitive Two-Pore Na+ Channels to Adapt to Metabolic State

Cang C. et al. Cell, 152 (2013) 778-790.

http://www.sciencedirect.com/science/article/pii/S0092867413000755

Ted Ho (Biophysics)

FOXO3A directs a protective autophagy program in haematopoietic stem cells

Warr, M. et al. Nature 494, 323-327 (21 February 2013).

http://www.nature.com/nature/journal/v494/n7437/full/nature11895.html

Academic YEAR 2012

Date Speaker 1 Speaker 2 Details
9/27/11 BBC Orientation
10/4/11 Javona WhiteBear (Bioinformatics) Chris Williams (CCB)

Chris Williams (CCB)

RNA Mimics of Green Flurorescent Protein. Paige et al. Science 333, 642-646 (2011).

10/11/11 David Paquette (Biophysics) Elizabeth Reuman (Bioinformatics)

David Paquette (Biophysics)

Cho, Jae-Hyun, et al. Tuning protein autoinhibition by domain destabilization. NSMB. 18, 550-555 (2011)

Elizabeth Reuman (Bioinformatics)

lincRNAs act in the circuitry controlling pluripotency and differentiation. Guttman M, Donaghey J, Carey BW, Garber M, Grenier JK, Munson G, Young G, Lucas AB, Ach R, Bruhn L, Yang X, Amit I, Meissner A, Regev A, Rinn JL, Root DE, Lander ES. Nature. 2011 Aug 28;477(7364):295-300.

10/18/11 Chris Novotny (CCB) Catherine Shi (Biophysics)

Chris Novotny (CCB)

BRCA1 tumour suppression occurs via heterochromatin-mediated silencing" from the September issue of Nature

Catherine Shi (Biophysics)

Focused Evolution of HIV-1 Neutralizing Antibodies Revealed by Structures and Deep Sequencing from the 16 Sept 2011 issue of Science.

10/25/11 Flora Rutaganira (CCB) Natalia Khuri (Biophysics)

Flora Rutaganira (CCB)

Successful Establishment of Wolbachia in Aedes Populations to Suppress Dengue Transmission" Hoffmann AA et al. Nature (476) 454 - 457. August 2011

Natalia Khuri (Biophysics)

Stochastic state transitions give rise to phenotypic equilibrium in populations of cancer cells" by Eric Lander's group, published in Cell (August 2011):

11/1/11 Hai Tran (CCB) Yi Song (Bioinformatics)

Hai Tran (CCB)

Acceleration of Emergence of Bacterial Antibiotic Resistance in Connected Microenvironments. Zhang et. al. Science 333, 1763-1767 (2011).

Yi Song (Bioinformatics)

Article Title: The Dynamic Architecture of Hox Gene Clusters Author: Daan Noordermeer, Marion Leleu, Erik Splinter, Jacques Rougemont, Wouter De Laat, Denis Duboule Journal Name: Science Journal Issue/Pages: VOL334/222-225 Month Year: 10/2011

11/8/11 Yi-Chang Liu (CCB) Liz Howe (Bioinformatics)

Yi-Chang Liu (CCB)

1 Bonger, K.M., Chen, L.C., Liu, C.W., & Wandless, T.J., Small-molecule displacement of a cryptic degron causes conditional protein degradation. Nat Chem Biol 7 (8), 531-537. 2 Neklesa, T.K. et al., Small-molecule hydrophobic tagging-induced degradation of HaloTag fusion proteins. Nat Chem Biol 7 (8), 538-543.

11/15/11 Brittany Fotsch (CCB) David Mavor (iPQB)

Brittany Fotsch (CCB)

Complement factor H binds malondialdehyde epitopes and protects from oxidative stress. Weissmann, et. al. Nature 478, 76-81 (06 October 2011)

David Mavor (iPQB)

Duderstadt et al Nature, 478:209 'DNA stretching by bacterial initiators promotes replication origin opening'

11/22/11 Justin Meyerowitz (CCB) John Haliburton (iPQB)

Justin Meyerowitz (CCB)

Organization of intracellular reactions with rationally designed RNA assemblies. Delebecque CJ, Lindner AB, Silver PA, Aldaye FA. Science 333:470-474; July 2011.

John Haliburton (iPQB)

Drosophila Microbiome Modulates Host Developmental and Metabolic Homeostasis via Insulin Signaling Seung Chul Shin, et al. Science 334, 670 (2011); DOI: 10.1126/science.1212782

11/29/11 Daniel Himmelstein (iPQB) Noah Younger (CCB)

Daniel Himmelstein (iPQB)

Alterovitz et al. Ontology engineering. Nature Biotechnology 28, 128 130, (2010)

Noah Younger (CCB)

Selective killing of cancer cells by a small molecule targeting the stress response to ROS Lakshmi Raj, et. al Nature Vol. 475, pp 231-234 July 2011

1/3/12 Katherine Aull (iPQB) Weihan Li (iPQB)

Katherine Aull (iPQB)

Dynamic Exchange at Regulatory Elements during Chromatin Remodeling Underlies Assisted Loading Mechanism, Voss et al, Cell 2011 Do transcription factors "hit and run"?

Weihan Li (iPQB)

Growth Rate-Dependent Global Effects on Gene Expression in Bacteria Stefan Klumpp, Zhongge Zhang, and Terence Hwa Cell 139, 1366–1375, 2009

1/10/12 Rebecca Levin (CCB) Thomas Stevens (iPQB)

Rebecca Levin (CCB)

A genetically incorporated crosslinker reveals chaperone cooperation in acid resistance. Nature Chemical Biology 7, 671–677 (2011)

Thomas Stevens (iPQB)

Rechavi, O., Minevich, G., & Hobert, O. (2011). Transgenerational Inheritance of an Acquired Small RNA-Based Antiviral Response in C. elegans. Cell, 1-9.

1/17/12 Benjamin Spangler (CCB) Amy Chang (iPQB)

Benjamin Spangler (CCB)

Chemically Crosslinking the Active Site of O-GlcNAc transferase. A neutral diphosphate mimic crosslinks the active site of human O-GlcNAc transferase by Jiang, et al., in Nature Chem. Bio. Released online November 13, 2011.

Amy Chang (iPQB)

Electrical Spiking in Escherichia coli Probed with a Fluorescent Voltage-Indicating Protein by Kralj et al., in Science. Published July 15, 2011.

1/24/12 Megan Li (PSPG) Patrick Harrigan (iPQB)

Megan Li (PSPG)

Leuschner F et al. Therapeutic siRNA silencing in inflammatory monocytes in mice. Nat Biotechnol. 2011 Nov; 29(11):1005-10.

Patrick Harrigan (iPQB)

Predicting mutation outcome from early stochastic variation in genetic interaction partners from nature, december 2011

1/31/12 Ben Heineike (iPQB) Ryan Conrad (PSPG)

Ben Heineike (iPQB)

A sensing array of radically coupled genetic 'biopixels'. Prindle A, Samayoa P, Razinkov I, Danino T, Tsimring LS, Hasty J. 1. Nature. 2011 Dec 18;481(7379):39-44. doi: 10.1038/nature10722. Department of Bioengineering, University of California, San Diego, La Jolla, California 92093, USA.

Ryan Conrad (PSPG)

SIRT6 Promotes DNA Repair Under Stress by Activating PARP1 Mao et al. Science 17 June 2011: Vol. 332 no. 6036 pp. 1443-1446

2/7/12 Rahel Woldeyes (CCB) Sara Calhoun (iPQB)

Rahel Woldeyes (CCB)

HIV-1 restriction factor SAMHD1 is a deoxynucleoside triphosphate triphosphohydrolase. Goldstone, D. C., Ennis-Adeniran, V., Hedden, J. J., Groom, H. C. T., Rice, G. I., Christodoulou, E., et al. (2011). Nature, 480, 379-382.

Sara Calhoun (iPQB)

Hot Spots for Allosteric Regulation on Protein Surfaces. Reynolds, K.A., McLaughlin, R.N., and Ranganathan, R. (2011) Cell, 147:1564-1575.

2/14/12 Jaun Perez Bermejo (iPQB) Rose Citron (iPQB)

Jaun Perez Bermejo (iPQB)

Love in the Time of Chagas. "Cytokine-dependent and –independent gene expression changes and cell cycle block revealed in Trypanosoma cruzi-infected host cells by comparative mRNA profiling." Costales JA, Daily JP, Burleigh BA. BMC Genomics 2009, 10:252

Rose Citron (iPQB)

Science 334, 1723 (2011); Christian M. Kaiser, et al. The Ribosome Modulates Nascent Protein Folding

2/21/12 Jordan Carelli (CCB) Peter Fellowes (iPQB)

Jordan Carelli (CCB)

Morckel, a. R., Lusic, H., Farzana, L., Yoder, J. a., Deiters, a., and Nascone-Yoder, N. M. (2011) A photoactivatable small-molecule inhibitor for light-controlled spatiotemporal regulation of Rho kinase in live embryos, Development 139, 437-442.

Peter Fellowes (iPQB)

Non-genetic heterogeneity from stochastic partitioning at cell division", Huh and Paulsson

2/28/12 Louise Goupil (CCB) Robert Schiemann (iPQB)

Louise Goupil (CCB)

Peroxide-dependent sulfenylation of the EGFR catalytic site enhances kinase activity. Paulsen, C.E. et al. Nature Chemical Biology 8, 57-64 (2011).

Robert Schiemann (iPQB)

"RNA Editing Underlies Temperature Adaptation in K+ Channels from Polar Octopuses" http://www.sciencemag.org/content/early/2012/01/04/science.1212795

3/6/12 Adrian Stecula (PSPG) Javona WhiteBear (BMI) (Bioinformatics)

Adrian Stecula (PSPG)

Stephens, Philip J, Chris D Greenman, Beiyuan Fu, Fengtang Yang, Graham R Bignell, Laura J Mudie, Erin D Pleasance, et al. 2011. “Massive Genomic Rearrangement Acquired in a Single Catastrophic Event during Cancer Development.” Cell 144 (1) (January 7): 27–40. doi:10.1016/j.cell.2010.11.055.

Javona WhiteBear (BMI) (Bioinformatics)

Fasting Cycles Retard Growth of Tumors and Sensitize a Range of Cancer Cell Types to Chemotherapy Changhan Lee, Lizzia Raffaghello, Sebastian Brandhorst, Fernando M. Safdie, Giovanna Bianchi, Alejandro Martin-Montalvo, Vito Pistoia, Min Wei, Saewon Hwang, Annalisa Merlino, Laura Emionite, Rafael de Cabo, and Valter D. Longo Sci Transl Med 3003293. published ahead of print 8 February 2012, [DOI:10.1126/scitranslmed.3003293]

3/13/12 Nicole Olson (CCB) Greg Fedewa (iPQB)

Nicole Olson (CCB)

Widespread Genetic Switches and Toxicity Resistance Proteins for Fluoride Science, 13 January 2012, 335 (6065): 233-235.

Greg Fedewa (iPQB)

Flavor network and the principles of food pairing * Yong-Yeol Ahn,1, 2, 3, 5 * Sebastian E. Ahnert,1, 4, 5 * James P. Bagrow1, 2 * & Albert-László Barabási1, 2 Journal name: Scientific Reports Volume: 1 Published 15 December 2011

3/27/12 Amy Jacobson (CCB) Kale Kundert (iPQB)

Amy Jacobson (CCB)

Antiparallel EmrE exports drugs by exchanging between asymmetric structures. Morrison, E.A., et al. Nature 481, 45-50 (2012).

Kale Kundert (iPQB)

Identification of oxadiazoles as new drug leads for the control of schistosomiasis. Nature Medicine 14, 407 - 412 (2008)

4/3/12 Aishjay Jayagopal (PSPG) Tara Friedrich (iPQB)

Aishjay Jayagopal (PSPG)

First-in-Human Testing of a Wirelessly Controlled Drug Delivery Microchip, R. Farra et al, Science Translational Medicine, Feb 2012

Tara Friedrich (iPQB)

Multiple Epigenetic Modifiers Induce Aggressive Viral Extinction in Extraembryonic Endoderm Stem Cells Michael C. Golding, Liyue Zhang, Mellissa R.W. Mann

4/10/12 Sarah Woldemariam (CCB) Kyle Barlow (iPQB)

Sarah Woldemariam (CCB)

Critical Role of Amyloid-like Oligomers of Drosophila Orb2 in the Persistence of Memory (Cell, Volume 148, Pages 515-529, Published February 3, 2012)

Kyle Barlow (iPQB)

"Of mice and men: an Alzheimer's cure for our murine brethren" Cramer, Paige E, John R Cirrito, Daniel W Wesson, C. Y. Daniel Lee, J. Colleen Karlo, Adriana E Zinn, Brad T Casali, et al. "ApoE-Directed Therapeutics Rapidly Clear Β-Amyloid and Reverse Deficits in AD Mouse Models." Science 335, no. 6075 (March 23, 2012): 1503-1506.

4/17/12 Marian Deuker (CCB) Liz Howe (iPQB)

Marian Deuker (CCB)

Science. 2011 Dec 16;334(6062):1557-60. The molecular basis of acid insensitivity in the African naked mole-rat. Smith ES, Omerbašić D, Lechner SG, Anirudhan G, Lapatsina L, Lewin GR.

Liz Howe (iPQB)

Host Cell Invasion by Apicomplexan Parasites: Insights from the Co-Structure of AMA1 with a RON2 peptide

4/24/12 Alexander Pankov (iPQB) Christina Fitzsimmons (CCB)

Alexander Pankov (iPQB)

D. N. Reshef, Y. A. Reshef, H. K. Finucane, S. R. Grossman, G. McVean, P. J. Turnbaugh,E. S. Lander, M. Mitzenmacher, P. C. Sabeti. Detecting novel associations in large datasets. Science, 334: 1518-1524, (2011).

Christina Fitzsimmons (CCB)

To Knot or Not? Paper: A.L. Mallam & S.E. Jackson. Knot formation in newly translated proteins is spontaneous and accelerated by chaperonins. Nature Chemical Biology, 2012, 8, 147-153. doi: 10.1038/nchembio.742

5/1/12 Katherine Southard (CCB) Graham Heimberg (iPQB)

Katherine Southard (CCB)

Small-molecule-induced DNA damage identifies alternative DNA structures in human genes.<http://www.mendeley.com/library/showrecent/document/4651621063/#> Raphaël Rodriguez, Kyle M Miller, Josep V Forment, Charles R Bradshaw, Mehran Nikan, Sébastien Britton, Tobias Oelschlaegel, Blerta Xhemalce, Shankar Balasubramanian, Stephen P Jackson (2012) Nature chemical biology 8 (3) p. 301-10 http://www.nature.com/nchembio/journal/v8/n3/full/nchembio.780.html

Graham Heimberg (iPQB)

"The most expensive cold diagnosis ever." Paper: Personal Omics Profiling Reveals Dynamic Molecular and Medical Phenotypes Cell 148, 1293–1307, March 16, 2012 Rui Chen,1,11 George I. Mias,1,11 Jennifer Li-Pook-Than,1,11 Lihua Jiang,1,11 Hugo Y.K. Lam,1,12 Rong Chen,2,12 Elana Miriami,1 Konrad J. Karczewski,1 Manoj Hariharan,1 Frederick E. Dewey,3 Yong Cheng,1 Michael J. Clark,1 Hogune Im,1 Lukas Habegger,6,7 Suganthi Balasubramanian,6,7 Maeve O’Huallachain,1 Joel T. Dudley,2 Sara Hillenmeyer,1 Rajini Haraksingh,1 Donald Sharon,1 Ghia Euskirchen,1 Phil Lacroute,1 Keith Bettinger,1 Alan P. Boyle,1 Maya Kasowski,1 Fabian Grubert,1 Scott Seki,2 Marco Garcia,2 Michelle Whirl-Carrillo,1 Mercedes Gallardo,9,10 Maria A. Blasco,9 Peter L. Greenberg,4 Phyllis Snyder,1 Teri E. Klein,1 Russ B. Altman,1,5 Atul J. Butte,2 Euan A. Ashley,3 Mark Gerstein,6,7,8 Kari C. Nadeau,2 Hua Tang,1 and Michael Snyder1,*

5/8/12 Xiaoming Liang (PSPG) Stephen Nayfach-Battilana (iPQB)

Xiaoming Liang (PSPG)

A PGC1-&#945;-dependent myokine that drives brown-fat-like development of white fat and thermogenesis. 2012 Jan 11;481(7382):463-8. Nature. Bostrom P. et al.

Stephen Nayfach-Battilana (iPQB)

Untangling Genomes from Metagenomes: Revealing an Uncultured Class of Marine Euryarchaeota

5/15/12 Russell Goodman (iPQB) James Webber (iPQB)

Russell Goodman (iPQB)

Quantifying internal friction in unfolded and intrinsically disordered proteins with single-molecule spectroscopy. Soranno A. et al., Proc Natl Acad Sci. 2012 Apr 6.

James Webber (iPQB)

DNA breaks and chromosome pulverization from errors in mitosis. Crasta K et al, Nature. 2012 Feb 2; 482(7383):53-8

5/22/12 Andrew Van Benschoten (iPQB) Naomi Yonis (CCB)

Andrew Van Benschoten (iPQB)

Sexual Deprivation Increases Ethanol Intake in Drosophila (Shohat-Ophir et.al, Science, 2012 Mar 16;335(6074):1351-5).

Naomi Yonis (CCB)

The article I will present is: "Atg7 Modulates p53 Activity to Regulate Cell Cycle and Survival During Metabolic Stress". (http://www.sciencemag.org/content/336/6078/225.full) The citation is: Lee, I.H. et al. Atg7 Modulates p53 Activity to Regulate Cell Cycle and Survival During Metabolic Stress. Science, 336, 225 (2012).

5/29/12 Yu Yue (iPQB) Diego Garrido Ruiz (iPQB)

Yu Yue (iPQB)

Evolution of Human-Specific Neural SRGAP2 Genes by Incomplete Segmental Duplication Megan Y. Dennis,1,8 Xander Nuttle,1,8 Peter H. Sudmant,1 Francesca Antonacci,1 Tina A. Graves,3 Mikhail Nefedov,4 Jill A. Rosenfeld,5 Saba Sajjadian,1 Maika Malig,1 Holland Kotkiewicz,3 Cynthia J. Curry,6 Susan Shafer,7 Lisa G. Shaffer,5 Pieter J. de Jong,4 Richard K. Wilson,3 and Evan E. Eichler1,2,* 1Department of Genome Sciences 2Howard Hughes Medical Institute University of Washington School of Medicine, Seattle, WA 98195, USA 3The Genome Institute at Washington University, Washington University School of Medicine, St. Louis, MO 63110, USA 4Children’s Hospital Oakland Research Institute, Children’s Hospital and Research Center at Oakland, Oakland, CA 94609, USA 5Signature Genomic Laboratories, PerkinElmer, Inc., Spokane, WA 99207, USA 6Genetic Medicine Central California, University of California, San Francisco, Fresno, CA 93701, USA 7Carle Clinic Association, Urbana, IL 61801, USA 8These authors contributed equally to this work *Correspondence: eee@gs.washington.edu DOI 10.1016/j.cell.2012.03.033

Diego Garrido Ruiz (iPQB)

Three-Dimensional Structures of Membrane Proteins from Genomic Sequencing Hopf, Thomas A., Colwell, Lucy J.,Sheridan, Robert, Rost, Burkhard, Sander, Chris, Marks, Debora S., Cell, May 2012

6/5/12 Jessica Thomaston

Jessica Thomaston

Experimental adaptation of an influenza H5 HA confers respiratoryrndroplet transmission to a reassortant H5 HA/H1N1 virus in ferretsrnMasaki Imai, Tokiko Watanabe, Masato Hatta, Subash C. Das, MakotornOzawa, Kyoko Shinya, Gongxun Zhong, Anthony Hanson, Hiroaki Katsura,rnShinji Watanabe, Chengjun Li, Eiryo Kawakami, Shinya Yamada, MakirnKiso, Yasuo Suzuki, Eileen A. Maher, Gabriele Neumann & YoshihirornKawaokarnNature (2012) doi:10.1038/nature10831 Published online 02 May 2012

Academic YEAR 2011

Date Speaker 1 Speaker 2 Details
9/28/10 Orientation

Orientation

BBC Journal Club Orientation with Program Directors

10/5/10 Aaron Mendez (CCB) Jonathan Gable (Biophysics)

Aaron Mendez (CCB)

Enhancement of the proteasome activity by a small-molecule inhibitor of USP14 Byung-Hoon Lee, Min Jae Lee, Soyeon Park, Dong-Chan Oh, Suzanne Elsasser, Ping-Chung Chen, Carlos Gartner, Nevena Dimova, John Hanna, Steven P. Gygi, Scott M. Wilson, Randall W. King & Daniel Finley

Jonathan Gable (Biophysics)

Endogenous non-retroviral RNA virus elements in mammalian genomes. Horie M, Honda T, Suzuki Y, Kobayashi Y, Daito T, Oshida T, Ikuta K, Jern P, Gojobori T, Coffin JM, Tomonaga K Nature 2010 Jan 7 463(7277):84-7

10/12/10 Joel Karpiak (CCB) Melanie Smith (Biophysics)

Joel Karpiak (CCB)

"Computational Design of an Enzyme Catalyst for a Stereoselective Bimolecular Diels-Alder Reaction" Science 16 July 2010: Vol. 329. no. 5989, pp. 309 - 313

Melanie Smith (Biophysics)

Yunger, S., Rosenfeld, L., Garini, Y., and Shav-Tal, Y. (2010) Single allele analysis of transcription kinetics in living mammalian cells. Nat Methods. 7(8): 631-3.

10/19/10 Peter Cimermancic (Bioinformatics) Crystal Nyitray (CCB)

Peter Cimermancic (Bioinformatics)

Bacterial charity work leads to population-wide resistance

Henry H. Lee, Michael N. Molla, Charles R. Cantor & James J. Collins. Nature, Volume: 467, Pages: 82- 85. Date published: (02 September 2010) DOI:10.1038/nature09354 Bacterial charity work leads to population-wide resistance * Henry H. Lee, * Michael N. Molla, * Charles R. Cantor * & James J. Collinsjcollins@bu.edu * Affiliations * Contributions * Corresponding author Journal name: Nature Volume: 467 , Pages: 82 - 85 Date published: (02 September 2010)

http://www.nature.com/nature/journal/v467/n7311/full/nature09354.html

Crystal Nyitray (CCB)

Influenza Virus M2 Protein Mediates ESCRT-Independent Membrane Scission Jeremy S. Rossman, Xianghong Jing, George P. Leser, Robert A. Lamb. Cell, 142:6, 902-17. 2010.

10/26/10 Charles Greenberg (Biophysics) Jonathan Ostrem (CCB)

Charles Greenberg (Biophysics)

Single-cell NF-kappaB dynamics reveal digital activation and analogue information processing. Tay S, Hughey JJ, Lee TK, Lipniacki T, Quake SR, Covert MW. Nature 466 267- 271 (08 July 2010)

Jonathan Ostrem (CCB)

Mammalian Expression of Infrared Fluorescent Proteins Engineered from a Bacterial Phytochrome Xiaokun Shu, Antoine Royant, Michael Z. Lin, Todd A. Aguilera, Varda Lev-Ram, Paul A. Steinbach, Roger Y. Tsien

11/9/10 Zac Apte (Biophysics) Laurens Kraal (Bioinformatics)

Zac Apte (Biophysics)

Brinkmann et al., "Neutrophil extracellular traps kill bacteria" Science (2004) vol. 303 (5663) pp. 1532-5

Laurens Kraal (Bioinformatics)

Creation of a bacterial cell controlled by a chemically synthesized genome. Gibson DG, Glass JI, Lartigue C, Noskov VN, Chuang RY, Algire MA, Benders GA, Montague MG, Ma L, Moodie MM, Merryman C, Vashee S, Krishnakumar R, Assad-Garcia N, Andrews-Pfannkoch C, Denisova EA, Young L, Qi ZQ, Segall-Shapiro TH, Calvey CH, Parmar PP, Hutchison CA 3rd, Smith HO, Venter JC. Science. 2010 Jul 2;329(5987):52-6. Epub 2010 May 20.

11/16/10 Ian Vaughn (CCB) Dan Kaemmerer (Biophysics)

Ian Vaughn (CCB)

Mediator and cohesin connect gene expression and chromatin architecture.

Dan Kaemmerer (Biophysics)

Nature Biotechnology: Rapid profiling of a microbial genome using mixtures of barcoded oligonucleotides Joseph R Warner1, Philippa J Reeder1, Anis Karimpour-Fard2, Lauren B A Woodruff1 & Ryan T Gill1

11/23/10 Amanda Silber (CCB) Zhiyuan Li (Biophysics)

Amanda Silber (CCB)

Schmidt, Mark, et al. Crucial role for human Toll-like receptor 4 in the development of contact allergy to nickel. (Sept 2010) Nature.

Zhiyuan Li (Biophysics)

A synthetic-natural hybrid oscillator in human cells, Toettcher et.al, 2010, PNAS,

1/4/11 Noel Jee (CCB) Aram Avila-Herrera (Bioinformatics)

Noel Jee (CCB)

A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus

Aram Avila-Herrera (Bioinformatics)

Thermal Enhancement with Optically Activated Gold Nanoshells Sensitizes Breast Cancer Stem Cells to Radiation Therapy

1/11/11 Si-Han Chen (Biophysics) Justin Rettenmaier (CCB)

Si-Han Chen (Biophysics)

Hailey et al. Mitochondria supply membranes for autophagosome biogenesis during starvation. Cell (2010) vol. 141 (4) pp. 656-67 http://www.ncbi.nlm.nih.gov/pubmed/20478256

Justin Rettenmaier (CCB)

A Model for Neural Development and Treatment of Rett Syndrome Using Human Induced Pluripotent Stem Cells Maria C.N. Marchetto,1,5 Cassiano Carromeu,2,5 Allan Acab,2 Diana Yu,1 Gene W. Yeo,3 Yangling Mu,1 Gong Chen,4 Fred H. Gage,1 and Alysson R. Muotri2,* CELL 143 527-539 Nov 2010

1/18/11 Melody Lee (CCB) Erik Jonsson (Biophysics)

Melody Lee (CCB)

Transmembrane Receptor DCC Associates with Protein Synthesis Machinery and Regulates Translation. Tcherkezian J et al. Cell (2010) 141: 632-644

Erik Jonsson (Biophysics)

How Cats Lap: Water Uptake by Felis catus by Reis et al. Science (2010)

1/25/11 Elizabeth Reuman Florentine Rutaganira (CCB)

Elizabeth Reuman

D-amino acids trigger biofilm disassembly. Kolodkin-Gal I, Romero D, Cao S, Clardy J, Kolter R, Losick R. Science. 2010 Apr 30;328(5978):627-9.

Florentine Rutaganira (CCB)

Selective inhibition of BET bromodomains Panagis Filippakopoulos et al. Nature Dec 2010

2/1/11 David Paquette Natalia Khuri

David Paquette

Ebbinghaus, S., Dhar, A., McDonald, J.D., and Gruebele, M. "Protein folding stability and dynamics imaged in a living cell." Nature Methods. 7, 319-323 (2010)

Natalia Khuri

"FOXA1 is a key determinant of estrogen receptor function and endocrine response" by Hurtado A, Holmes KA, Ross-Innes CS, Schmidt D, Carroll JS. Nat Genet. 2010 Dec 12.

2/8/11 Christopher Williams (CCB)

Christopher Williams (CCB)

Goldman N, Chen M, Fujita T, Xu Q, Peng W, Liu W, Jensen TK, Pei Y, Wang F, Han X, Chen JF, Schnermann J, Takano T, Bekar L, Tieu K, Nedergaard M. Adenosine A1 receptors mediate local anti-nociceptive effects of acupuncture. Nat Neurosci 2010;

2/15/11 Yi-Chang Liu (CCB) Alec Nielsen

Yi-Chang Liu (CCB)

"Inhibitors of protein disulfide isomerase suppress apoptosis induced by misfolded proteins." Hoffstrom, B.G. et al., Nat Chem Biol 6 (12), 900-906.

Alec Nielsen

Spatial organization of the flow of genetic information in bacteria. Llopis PM, Jackson AF, Silusarenko O, Surovtsev I, Heinritz J, Emonet T & Jacobs-Wagner C. Nature. 2010 Jul 1.

2/22/11 Chris Novotny (CCB)

Chris Novotny (CCB)

Circulating mitochondrial DAMPs cause inflammatory responses to injury" by Zhang et al. from the March 2010 edition of Nature.

3/1/11 Brittany Fotsch (CCB) Catherine Shi

Brittany Fotsch (CCB)

Structure of human O-GlcNAc transferase and its complex with a peptide substrate. Lazarus MB, Nam Y, Jiang J, Sliz P, & Walker S. Nature 469, 564-567 (27 January 2011) http://www.nature.com/nature/journal/v469/n7331/full/nature09638.html

Catherine Shi

An interdomain sector mediating allostery in Hsp70 molecular chaperones Robert G Smock,1 Olivier Rivoire,2 William P Russ,3 Joanna F Swain,1*Stanislas Leibler,2,4 Rama Ranganathan,a3 and Lila M Gieraschb1,5 Nature Molecular Systems Biology 21 Sept 2010

3/8/11 Yi Song (Bioinformatics) Hai Tran (CCB)

Yi Song (Bioinformatics)

Rewiring of Genetic Networks in Response to DNA Damage Sourav Bandyopadhyay, et al. Science December 2010: Vol. 330 no. 6009 pp. 1385-1389

Hai Tran (CCB)

Jan 28, 2011 issue of Science entitled "Metagenomic Discovery of Biomass-Degrading Genes and Genomes from Cow Rumen"

3/29/11 Javona White Bear
3/29/11 Elizabeth Howe Javona White Bear
4/5/11 Elizabeth Howe (Bioinformatics)

Academic YEAR 2010

Date Speaker 1 Speaker 2 Details
9/29/09 BBC Orientation
10/6/09 Genevieve Erwin Megan Riel-Mehan

Genevieve Erwin

Functional Characterization of the Antibiotic Resistance Reservoir in the Human Microflora, by Morten O. A. Sommer, Gautam Dantas, and George M. Church, from Science (Aug 28, 2009)

Megan Riel-Mehan

Chemical Dissection of an Essential Redox Switch in Yeast Candice E. Paulsen1 and Kate S. Carroll1,2,3,* 1Chemical Biology Graduate Program 2Department of Chemistry 3Life Sciences Institute University of Michigan, Ann Arbor, MI 48109-2216, USA *Correspondence: katesc@umich.edu DOI 10.1016/j.chembiol.2009.01.003

10/13/09 Charlie Morgan (CCB) Geoff Rollins (Biophysics)

Charlie Morgan (CCB)

"Visualization of ATP levels inside single living cells with fluorescence resonance energy transfer-based genetically encoded indicators" Imamura, H., et al. PNAS Sept 15 2009.

Geoff Rollins (Biophysics)

Origins and evolutionary genomics of the 2009 swine-origin H1N1 influenza A epidemic Smith et al. Nature 459, 1122-1125 (2009)

10/20/09 Joanna Lipinski (Bioinformatics) Edwin Rodriguez (Biophysics)

Joanna Lipinski (Bioinformatics)

"Programming cells by multiplex genome engineering and accelerated evolution" Wang H, Isaacs F, Carr P, Sun Z, Xu G, Forest C, Church G. Nature 460, 894-898 (13 August 2009)

Edwin Rodriguez (Biophysics)

An Unfolded CH1 Domain Controls the Assembly and Secretion of IgG Antibodies

10/27/09 Idelisse Ortiz Torres (CCB) Chris Fuller (Bioinformatics)

Idelisse Ortiz Torres (CCB)

Tankyrase inhibition stabilizes axin and antagonizes Wnt signalling Nature 461, 614-620 (1 October 2009) | doi:10.1038/nature08356;

Chris Fuller (Bioinformatics)

"Unbiased Reconstruction of a Mammalian Transcriptional Network Mediating Pathogen Responses" by Ido Amit, et al. It's in the October 9th issue of Science.

11/3/09 Dan Lu (Biophysics) Dan Le (CCB)

Dan Lu (Biophysics)

Protein sectors: evolutionary units of three-dimensional structure. Najeeb Halabi, Olivier Rivoire, Stanislas Leibler, Rama Ranganathan. Cell vol. 138 (4) pp. 774-86 (August 21, 2009)

Dan Le (CCB)

Inhibitors selective for mycobacterial versus human proteasomes Gang Lin et al Nature, Vol 461, 1 October 2009: pg 621-27

11/10/09 Henry Lin (Bioinformatics) Andrew Wiser (CCB)

Henry Lin (Bioinformatics)

I plan on doing my journal club (Nov 10th) talk on a paper titled: Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome Erez Lieberman-Aiden, et al. Science 326: 5950. 289-293. Oct 9, 2009

Andrew Wiser (CCB)

HDAC2 negatively regulates memory formation and synaptic plasticity" from Nature; vol 459; May 7, 2009

1/5/10 Ryan Gile (Bioinformatics) Samuel Myers (CCB)

Ryan Gile (Bioinformatics)

Sensing chromosome bi-orientation by spatial separation of aurora B kinase from Kinetochore substrates. Liu D, Vader G, Vromans MJ, Lampson MA, Lens SM Science 2009 Mar 6 323(5919):1350-3

Samuel Myers (CCB)

Distinct Self-Renewal and Differentiation Phases in the Niche of Infrequently Dividing Hair Follicle Stem Cells Ying V. Zhang1, Janice Cheong1, 2, Nichita Ciapurin1, 2, David J. McDermitt1 and Tudorita Tumbar Published online: August 6, 2009 Cell Stem Cell

1/12/10 James Kraemer (Biophysics) Russell Spitzer (Bioinformatics)

James Kraemer (Biophysics)

RNA-Guided RNA Cleavage by a CRISPR RNA-Cas Protein Complex Caryn R. Hale, Peng Zhao, Sara Olson, Michael O. Duff, Brenton R. Graveley, Lance Wells, Rebecca M. Terns, Michael P. Terns Cell p 945, Nov 24, 2009

Russell Spitzer (Bioinformatics)

Barrick and Lenski. Genome-wide Mutational Diversity in an Evolving Population of Escherichia coli. Cold Spring Harbor symposia on quantitative biology (2009)

1/19/10 Emmanuel Yera (Bioinformatics) Linh Ho (CCB)

Emmanuel Yera (Bioinformatics)

RNAi in Budding Yeast Ines A. Drinnenberg 1, David E. Weinberg 2, Kathleen T. Xie 2, Jeffrey P. Mower 3, Kenneth H. Wolfe 4, Gerald R. Fink 5, David P. Bartel 2*

Linh Ho (CCB)

Phosphoproteomics reveals new ERK MAP kinase targets and links ERK to nucleoporin-mediated nuclear transport Nature Structural & Molecular Biology 16, 1026 - 1035 (2009) Published online: 20 September 2009

1/26/10 Rocco Varela (Bioinformatics) Justin Rettenmaier (CCB)

Rocco Varela (Bioinformatics)

James B. Moseley, Adeline Mayeux, Anne Paoletti & Paul Nurse, A spatial gradient coordinates cell size and mitotic entry in fission yeast, Nature. 2009 Jun 11; 459(7248):782-3.

Justin Rettenmaier (CCB)

Direct inhibition of the NOTCH transcription factor complex Moellering RE, Cornejo M, Davis TN, Bianco CD, Aster JC, Blacklow SC, Kung AL, Gilliland DG, Verdine GL, Bradner JE. Nature p182, Nov 12, 2009.

2/2/10 Melody Lee (CCB) Zac Apte (Biophysics)

Melody Lee (CCB)

Regulation of Inflammatory Responses by Gut Microbiota and Chemoattractant Receptor GPR43: Fiber, Fats, and Fun in the Gut: Regulation of Inflammatory Responses by Gut Microbiota and Chemoattractant Receptor GPR43

Zac Apte (Biophysics)

Conductivity of a single DNA duplex bridging a carbon nanotube gap. Nature Nanotechnology 2008 vol. 3 (3) pp. 163-7.

2/9/10 Erik Jonsson (Biophysics) Amanda Silber (CCB)

Erik Jonsson (Biophysics)

An RNA-dependent RNA polymerase formed by TERT and the RMRP RNA, Nature, 10 September 2009

Amanda Silber (CCB)

Aire's Partners in the Molecular Control of Immunological Tolerance. Jakub Abramson, Matthieu Giraud, Christophe Benoist, Diane Mathis. Cell. Vol. 140 (1), 8 January 2010, p 123-135.

2/16/10 Laurens Kraal Ian Vaughn

Laurens Kraal

Transcriptome complexity in a genome-reduced bacterium. Science 326: 1268

Ian Vaughn

Nuclear REceptor-Induced Chromosomal Proximity and DNA Breaks Underlie Specific Translocations in Cancer' (Lin et al. Cell, 2009).

2/23/10 Noel Jee (CCB) Jonathan Gable (Biophysics)

Noel Jee (CCB)

Monoacylglycerol Lipase Regulates a Fatty Acid Network that Promotes Cancer Pathogenesis

Jonathan Gable (Biophysics)

Antibody Recognition of a Highly Conserved Influenza Virus Epitope", Ekiert et al, Science 324, 246-251 (2009)

3/2/10 Jon Ostrem (CCB)

Jon Ostrem (CCB)

Shian-Huey Chiang, Merlijn Bazuine, Carey N. Lumeng, Lynn M. Geletka, Jonathan Mowers, Nicole M. White, Jing-Tyan Ma, Jie Zhou, Nathan Qi, Dan Westcott, Jennifer B. Delproposto, Timothy S. Blackwell, Fiona E. Yull, Alan R. Saltiel. The Protein Kinase Regulates Energy Balance in Obese Mice. (2009) Cell 138:961-75

3/9/10 Zhiyuan Li (Biophysics) Aaron Mendez (CCB)

Zhiyuan Li (Biophysics)

The ploarisome is required for segregation and retrograde transport of protein aggregates,2010, Beidong Liu, Cell.

Aaron Mendez (CCB)

Directed Evolution and Structural Characterization of a Simvastatin Synthase. Xue Gao, Xinkai Xie, Inna Pashkov,Michael R. Sawaya, Janel Laidman, Wenjun Zhang, Ralph Cacho, Todd O. Yeates, and Yi Tang

3/30/10 Peter Cimermancic (Bioinformatics) Crystal Nyitray (CCB)

Peter Cimermancic (Bioinformatics)

Nature 460, 711-716 (6 August 2009) | doi:10.1038/nature08237; Received 11 May 2009; Accepted 22 June 2009 Architecture and secondary structure of an entire HIV-1 RNA genome Joseph M. Watts1, Kristen K. Dang2, Robert J. Gorelick5, Christopher W. Leonard1, Julian W. Bess Jr5, Ronald Swanstrom3, Christina L. Burch4 & Kevin M. Weeks1

Crystal Nyitray (CCB)

A biological quarter-wave retarder with excellent achromacity in the visible wavelength region. Nature Photonics 3, 641 - 644 (2009) Published online: 25 October 2009 | doi:10.1038/nphoton.2009.189 N. W. Roberts1,2, T.-H. Chiou3, N. J. Marshall3 & T. W. Cronin4

4/6/10 Melanie Smith (Biophysics) Joel Karpiak (CCB)

Melanie Smith (Biophysics)

Gouridis, G., Karamanou, S., Gelis, I., Kalodimos, C.G., Economou, A. Signal peptides are allosteric activators of the protein translocase. (2009) Nature 462:363-7.

Joel Karpiak (CCB)

Conformational Spread as a Mechanism for Cooperativity in the Bacterial Flagellar Switch Fan Bai, Richard W. Branch, Dan V. Nicolau, Jr., Teuta Pilizota, Bradley C. Steel, Philip K. Maini, Richard M. Berry. Science 327, 685 - 689 (2010).

4/13/10 Charles Greenberg (Biophysics) Roxana Ordonez (Bioinformatics)

Charles Greenberg (Biophysics)

Ren Y, Yip CK, Tripathi A, Huie D, Jeffrey PD, Walz T, Hughson FM. A Structure-Based Mechanism for Vesicle Capture by the Multisubunit Tethering Complex Dsl1. (2009) Cell 139:1119-1129.

Roxana Ordonez (Bioinformatics)

Direct conversion of fibroblasts to functional neurons by defined factors Nature 463, 1035-1041 (25 February 2010)

4/20/10 Anthony Shiver (Biophysics) Daniel Kaemmerer (CCB)

Anthony Shiver (Biophysics)

Ettwig K et al Nitrite-driven anaerobic methane oxidation by oxygenic bacteria Nature 464:7288 (2010).

Daniel Kaemmerer (CCB)

http://www.nature.com/nchembio/journal/v6/n2/full/nchembio.280.html An in vitro translation, selection and amplification system for peptide nucleic acids

4/27/10 Si-Han Chen (Biophysics) Aram Avila-Herrera (Bioinformatics)

Si-Han Chen (Biophysics)

Danino et al. A synchronized quorum of genetic clocks. Nature (2010) vol. 463 (7279) pp. 326-30 article url http://www.nature.com/nature/journal/v463/n7279/full/nature08753.html

Aram Avila-Herrera (Bioinformatics)

Tetherin Inhibits HIV-1 Release by Directly Tethering Virions to Cells David Perez-Caballero1, 2, Trinity Zang1, 2, 3, Alaleh Ebrahimi1, 2, Matthew W. McNatt1, 2, Devon A. Gregory4, Marc C. Johnson4 and Paul D. Bieniasz1, 2, 3, http://www.cell.com/abstract/S0092-8674(09)01113-1

Academic YEAR 2009

Date Speaker 1 Speaker 2 Details
9/23/08 BBC Journal Club Organizational Meeting
9/30/08 Monica Tremont (Biophysics) Michael Lopez (CCB)

Monica Tremont (Biophysics)

Electron Relay in Proteins

Tryptophan-Accelerated Electron Flow Through Proteins. Shih C, Museth AK, Abrahamsson M, Blanco-Rodriguez AM, Di Bilio AJ, Sudhamsu J, Crane BR, Ronayne KL, Towrie M, Vlcek A, Richards JH, Winkler JR, Gray HB. Science 2008 Jun 27 320(5884):1760-2

Michael Lopez (CCB)

S-nitrosylation of the histone deacetylase 2 induces chromatin remodelling in neurons

Nott, Alexi et al. S-nitrosylation of the histone deacetylase 2 induces chromatin remodelling in neurons. Nature. Advanced online publication, (2008).

10/7/08 Noah Ollikainen (Bioinformatics) Gabe Rocklin (Biophysics)

Noah Ollikainen (Bioinformatics)

In vivo reprogramming of adult pancreatic exocrine cells to beta-cells

Zhou Q, Brown J, Kanarek A, Rajagopal J, Melton DA. In vivo reprogramming of adult pancreatic exocrine cells to beta-cells. Nature advance online publication 27 August 2008.

Gabe Rocklin (Biophysics)

Crowded, cell-like environment induces shape changes in aspherical protein

Crowded, cell-like environment induces shape changes in aspherical protein. Dirar Homouz, Michael Perham, Antonios Samiotakis, Margaret S. Cheung, and Pernilla Wittung-Stafshede, PNAS August 19, 2008 vol. 105 no. 33 11754-11759

10/14/08 Nicholas Hertz (CCB) Adam Marko (Bioinformatics)

Nicholas Hertz (CCB)

A double S Shape Provides the Structural Basis for the Extraordinary Binding Specificity of Dscam Isoforms

Michael R. Sawaya, Wof M. Wojtowicz, Ingemar Andre, Bin Qian, Wei Wu, David Baker, David Eisenberg, S. Lawrence Zipursky (2008). A double S Shape Provides the Structural Basis for the Extraordinary Binding Specificity of Dscam Isoforms. Cell 134, 1007-1018

Adam Marko (Bioinformatics)

It's all in your head: The Drosophila pheromone cVA activates a sexually dimorphic neural circuit

Sandeep Robert Datta, Maria Luisa Vasconcelos, Vanessa Ruta, Sean Luo, Allan Wong, Ebru Demir, Jorge Flores, Karen Balonze, Barry J. Dickson & Richard Axel. The Drosophila pheromone cVA activates a sexually dimorphic neural circuit. Nature 452, 473-477 (27 March 2008) doi:10.1038/nature06808.

http://www.nature.com/nature/journal/v452/n7186/full/nature06808.html

10/21/08 Cheryl Tajon (CCB) Jennifer Hsiao (Biophysics)

Cheryl Tajon (CCB)

The effect of particle design on cellular internalization pathways

Stephanie E. A. Gratton, Patricia A. Ropp, Patrick D. Pohlhaus, J. Christopher Luft, Victoria J. Madden, Mary E. Napier, and Joseph M. DeSimone. The effect of particle design on cellular internalization pathways. PNAS

Jennifer Hsiao (Biophysics)

Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions

"Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions." Guelen L, Pagie L, Brasset E, Meuleman W, Faza MB, Talhout W, Eussen BH, de Klein A, Wessels L, de Laat W, van Steensel B. Nature. 2008 Jun 12;453(7197):948-51. Epub 2008 May 7.

10/28/08 David Burkhardt (Biophysics) Rebecca Maglathlin (CCB)

David Burkhardt (Biophysics)

The 3D Structure of the Immunoglobulin Heavy-Chain Locus: Implications for Long-Range Genomic Interactions

S. Jhunjhunwala, M. van Zelm, M. Peak, S. Cutchin, R. Riblet, J. van Dongen, F. Grosveld, T. Knoch, C. Mur. The 3D Structure of the Immunoglobulin Heavy-Chain Locus: Implications for Long-Range Genomic Interactions. Cell, Volume 133, Issue 2, Pages 265-279.

Rebecca Maglathlin (CCB)

"An Alternative Menaqinone Biosynthetic Pathway Operating in Microorganisms"

"An Alternative Menaqinone Biosynthetic Pathway Operating in Microorganisms" Hiratsuka, et. al., Science, 321, 1670 (2008):DOI: 10.1126/science.1160446

11/4/08 Bethany Simmons (Bioinformatics) Jaline Gerardin (Biophysics)

Bethany Simmons (Bioinformatics)

Tissue deformation modulates twist expression to determine anterior midgut differentiation in Drosophila embryos

Tissue deformation modulates twist expression to determine anterior midgut differentiation in Drosophila embryos. Desprat N, Supatto W, Pouille PA, Beaurepaire E, Farge E Dev Cell 2008 Sep 15(3):470-7

Jaline Gerardin (Biophysics)

A mechanism for asymmetric segregation of age during yeast budding

Shcheprova Z, Baldi S, Frei SB, Gonnet G, Barral Y. A mechanism for asymmetric segregation of age during yeast budding. Nature. 2008 Aug 7;454(7205):728-34.

11/18/08 Brandon Butler (CCB) Elaine Kirschke (Biophysics)

Brandon Butler (CCB)

Cathepsin L Proteolytically Processes Histone H3 During Mouse Embryonic Stem Cell Differentiation

EM Duncan, TL Muratore-Schroeder, RG Cook, BA Garcia, J Shabanowitz, DF Hunt, and CD Allis. Cathepsin L Proteolytically Processes Histone H3 During Mouse Embryonic Stem Cell Differentiation. Cell, Volume 135, Issue 2, 284-294, 17 October 2008. doi:10.1016/j.cell.2008.09.055

Elaine Kirschke (Biophysics)

XPD Helicase Structures and Activities: Insights into the Cancer and Aging Phenotypes from XPD Mutations

XPD Helicase Structures and Activities: Insights into the Cancer and Aging Phenotypes from XPD Mutations. Li Fan, Jill O. Fuss, Quen J. Cheng, Andrew S. Arvai, Michal Hammel, Victoria A. Roberts, Priscilla K. Cooper and John A. Taine. Cell, Vol 133, Issue 5, 30 May 2008

11/25/08 Hannes Braberg (Biophysics) Robin Aglietti (CCB)

Hannes Braberg (Biophysics)

Stepwise chromatin remodelling by a cascade of transcription initiation of non-coding RNA

"Stepwise chromatin remodelling by a cascade of transcription initiation of non-coding RNAs". Kouji Hirota, Tomoichiro Miyoshi, Kazuto Kugou, Charles S. Hoffman, Takehiko Shibata & Kunihiro Ohta. Nature, Vol 456, 6 November 2008, doi:10.1038/nature07348.

Robin Aglietti (CCB)

The Acidic Repetitive Domain of the Magnetospirillum gryphiswaldense MamJ Protein Displays Hypervariability but Is Not Required for Magnetosome Chain Assembly

The Acidic Repetitive Domain of the Magnetospirillum gryphiswaldense MamJ Protein Displays Hypervariability but Is Not Required for Magnetosome Chain Assembly. Andr?© Scheffel and Dirk Sch?ºler. Journal of Bacteriology, September 2007, p. 6437-6446, Vol. 189, No. 17. doi:10.1128/JB.00421-07

1/6/09 Rand Miller (CCB)

Rand Miller (CCB)

CASK Functions as a Mg2+-independent Neurexin Kinase

CASK Functions as a Mg2+-independent Neurexin Kinase. Mukherjee, M. et al. Cell, Vol. 133, No. 2, April 18, 2008, p. 328-339

1/13/09 Heather Newman (Biophysics) Charlie Kehoe (Bioinformatics)

Heather Newman (Biophysics)

Label-Free Biomedical Imaging with High Sensitivity by Stimulated Raman Scattering Microscopy

Christian W. Freudiger, Wei Min, Brian G. Saar, Sijia Lu, Gary R. Holtom, Chengwei He, Jason C. Tsai, Jing X. Kang, and X. Sunney Xie. Label-Free Biomedical Imaging with High Sensitivity by Stimulated Raman Scattering Microscopy. Science 322 (5909), 1857. (19 December 2008) [DOI:10.1126/science.1165758]

Charlie Kehoe (Bioinformatics)

Structure and function of an RNase H domain at the heart of the spliceosome

Vladimir Pena, Alexey Rozov, Patrizia Fabrizio, Reinhard L?ºhrmann, and Markus C Wahl. Structure and function of an RNase H domain at the heart of the spliceosome. The EMBO Journal

http://dx.doi.org/10.1038/emboj.2008.209

1/20/09 George Peterson (Biophysics) Xiuming Wong (CCB)

George Peterson (Biophysics)

Tomas-Loba A, Flores I, Fernandez-Marcos PJ, Cayuela ML, Maraver A, Tejera A, Borras C, Matheu A, Klatt P, Flores JM, Vina J, Serrano M, Blasco MA. Telomerase Reverse Transcriptase Delays Aging in Cancer-Resistant Mice. Cell 135 (2008), 609-622.

Xiuming Wong (CCB)

Structural and Mechanistic Insights into STIM1-Mediated Initiation of Store-Operated Calcium Entry

Structural and Mechanistic Insights into STIM1-Mediated Initiation of Store-Operated Calcium Entry. P Li, MJ Plevin, M Ikura. Cell, Volume 135, Issue 1, 110-122, 3 October 2008

1/27/09 Peter Skewes-Cox (Bioinformatics) Carrie Shiau (CCB)

Peter Skewes-Cox (Bioinformatics)

Antigenic variation in Giardia lamblia is regulated by RNA interference. Nature. 2008 Dec 11;456(7223):750-4

Carrie Shiau (CCB)

DNA Demethylation in Zebrafish Involves the Coupling of a Deaminase, a Glycosylase, and Gadd45. Rai, K. et al. Cell, Vol 135, No. 7, December 26, 2008, p. 1201-1212.

2/3/09 Joe Kliegman (Biophysics) Chris Wen (Bioinformatics)

Joe Kliegman (Biophysics)

Sun et al. The structure of the phage T4 DNA packaging motor suggests a mechanism dependent on electrostatic forces. Cell (2008) vol. 135 (7) pp. 1251-62

Chris Wen (Bioinformatics)

Ashok Prasada,Julie Zikhermanb, Jayajit Dasa, Jeroen P. Roosec, Arthur Weissbd1 and Arup K. Chakrabortyaef1. Origin of the sharp boundary that discriminates positive and negative selection of thymocytes. PNAS January 13, 2009 vol. 106 no. 2 528-533

2/10/09 Brittany Belin (Biophysics) Jennifer Liu (CCB)

Brittany Belin (Biophysics)

Scott Smukalla, Marina Caldara, Nathalie Pochet, Anne Beauvais, Stephanie Guadagnini, Chen Yan, Marcelo D. Vinces, An Jansen, Marie Christine Prevost, Jean-Paul Latge, Gerald R. Fink, Kevin R. Foster, and Kevin J. Verstrepen. (2008) FLO1 Is a Variable Green Beard Gene that Drives Biofilm-like Cooperation in Budding Yeast. Cell 135(4), 726-737.

Jennifer Liu (CCB)

A tunable synthetic mammalian oscillator. Nature 457, 309-312 (15 January 2009)

2/17/09 David Booth (Biophysics) Jonathan Choy (CCB)

David Booth (Biophysics)

Byres E, et al. (4 Dec 2008) "Incorporation of a non-human glycan mediates human susceptibility to a bacterial toxin." Nature 456: 648-52.

Jonathan Choy (CCB)

AMPK and PPAR&#948; Agonists Are Exercise Mimetics.

Narkar, V. A., et al (2008). AMPK and PPAR&#948; Agonists Are Exercise Mimetics. Cell 134, 405-415. doi:10.1016/j.cell.2008.06.051

2/24/09 Daniel Le (CCB) Chris Fuller (Bioinformatics)

Daniel Le (CCB)

Yamagata K, Daitoku H, Takahashi Y, Namiki K, Hisatake K, Kako K, Mukai H, Kasuya Y, Fukamizu A. Arginine methylation of FOXO transcription factors inhibits their phosphorylation by Akt. Mol Cell. 2008 Oct 24;32(2):221-31.

Chris Fuller (Bioinformatics)

Genotype, haplotype and copy-number variation in worldwide human populations. Jakobsson, M. et al. Nature vol 451, 908-1002. 2008

3/3/09 Megan Riel-Mehan (CCB) Geoffrey Rollins (Biophysics)

Megan Riel-Mehan (CCB)

Science 28 November 2008: Vol. 322. no. 5906, pp. 1387 - 1392. An Epigenetic Role for Maternally Inherited piRNAs in Transposon Silencing. Julius Brennecke, Colin D. Malone, Alexei A. Aravin, Ravi Sachidanandam, Alexander Stark, Gregory J. Hannon.

Geoffrey Rollins (Biophysics)

Intersubunit coordination in a homomeric ring ATPase. Moffitt et al. Nature 457, 446-450 (2009).

3/10/09 Genevieve Erwin (Bioinformatics) Charles Morgan (CCB)

Genevieve Erwin (Bioinformatics)

ChIP-seq accurately predicts tissue-specific activity of enhancers. Axel Visel, Matthew J. Blow, Zirong Li, Tao Zhang, Jennifer A. Akiyama, Amy Holt, Ingrid Plajzer-Frick, Malak Shoukry, Crystal Wright, Feng Chen, Veena Afzal, Bing Ren, Edward M. Rubin & Len A. Pennacchio. Nature Vol 457| 12 February 2009| doi:10.1038/nature07730

Charles Morgan (CCB)

Quantitive exploration of the catalytic landscape separating divergent plant sesquiterpene synthases". Nature Chemical Biology. October(2008) Vol. 4 Number 10. pg. 617-623. O'Maille et. al.

3/31/09 Russell Spitzer (Bioinformatics) Edwin Rodriguez (Biophysics)

Russell Spitzer (Bioinformatics)

A stress-responsive RNA switch regulates VEGFA expression. Partho Sarothi Ray, Jie Jia, Peng Yao, Mithu Majumder, Maria Hatzoglou & Paul L. Fox Nature. 457. 915-919. 2009

Edwin Rodriguez (Biophysics)

Self-Sustained Replication of an RNA Enzyme. Science 323, 1229 (2009) Tracey A. Lincoln et al.

4/7/09 Emmanuel Yera (Bioinformatics)

Emmanuel Yera (Bioinformatics)

A TARBP2 mutation in human cancer impairs microRNA processing and DICER1 function. Sonia A Melo, Santiago Ropero, Catia Moutinho, Lauri A Aaltonen, Hiroyuki Yamamoto, George A Calin, Simona Rossi, Agustin F Fernandez, Fatima Carneiro, Carla Oliveira, Bibiana Ferreira, Chang-Gong Liu, Alberto Villanueva, Gabriel Capella, Simo Schwartz Jr, Ramin Shiekhattar & Manel Esteller. Nature Genetics 41, 365 - 370 (2009) Published online: 15 February 2009 | doi:10.1038/ng.317

4/14/09 Dan Lu (Biophysics) Roxana Ordonez (Bioinformatics)

Dan Lu (Biophysics)

Julien F Ayroles et al. Systems genetics of complex traits in Drosophila melanogaster. Nat Genet (2009) vol. 41 (3) pp. 299

Roxana Ordonez (Bioinformatics)

Cohen et al. Dynamic proteomics of individual cancer cells in response to a drug. Science (2008) vol. 322 (5907) pp. 1511-6

4/21/09 Andrew Wiser (CCB) Henry Lin (Bioinformatics)

Andrew Wiser (CCB)

"Monomeric fluorescent timers that change color from blue to red report on cellular trafficking". Subach et al. Nature Chemical Biology (2009) Volume 5 Number 2 February 2009 118-126

Henry Lin (Bioinformatics)

Variants of the Antibody Herceptin That Interact with HER2 and VEGF at the Antigen Binding Site. Jenny Bostrom, Shang-Fan Yu, David Kan, Brent A. Appleton, Chingwei V. Lee, Karen Billeci, Wenyan Man, Franklin Peale, Sarajane Ross, Christian Wiesmann, Germaine Fuh. Science 323, 1610 (2009)

4/28/09 Samuel Myers (CCB) Anthony Shiver (Biophysics)

Samuel Myers (CCB)

Histone h3 lysine 56 acetylation is linked to the core transcriptional network in human embryonic stem cells. Xie W, Song C, Young NL, Sperling AS, Xu F, Sridharan R, Conway AE, Garcia BA, Plath K, Clark AT, Grunstein M. Mol Cell. 2009 Feb 27;33(4):417-27.

Anthony Shiver (Biophysics)

Nature Structural & Molecular Biology. Helix Sliding in the stalk coiled coil of dynein couples ATPase and microtubule binding Takashide Kon et al. Vol 16 numb 3 march 2009

5/5/09 Joanna Lipinski (Bioinformatics) Idelisse Ortiz Torres (CCB)

Joanna Lipinski (Bioinformatics)

Non-genetic origins of cell-to-cell variability in TRAIL-induced apoptosis. Sabrina L. Spencer, Suzanne Gaudet, John G. Albeck, John M. Burke & Peter K. Sorger. (doi:10.1038/nature08012)

Idelisse Ortiz Torres (CCB)

Selective Erasure of a Fear Memory Jin-Hee Han, Steven A. Kushner, Adelaide P. Yiu, Hwa-Lin (Liz) Hsiang, Thorsten Buch, Ari Waisman, Bruno Bontempi, Rachael L. Neve, Paul W. Frankland, and Sheena A. Josselyn (13 March 2009) Science 323 (5920), 1492. [DOI: 10.1126/science.1164139]

5/12/09 Ryan Gile (Bioinformatics)

Ryan Gile (Bioinformatics)

Stretching Single Talin Rod Molecules Activates Vinculin Binding. Armando del Rio. Science (January 2009).

5/19/09 Linh Ho (CCB) James Kraemer (Biophysics)

Linh Ho (CCB)

Linh Ho: AMPK regulates energy expenditure by modulating NAD+ metabolism and SIRT1 activity Nature 458, 1056-1060, 2009.

James Kraemer (Biophysics)

Ligand-Dependent Equilibrium Fluctuations of Single Calmodulin Molecules. Jan Philipp Junker, Fabian Ziegler, and Matthias Rief. Science 30 January 2009: 633-637.

5/26/09 Rocco Varela (Bioinformatics) Kiyoshi Egami (Biophysics)

Rocco Varela (Bioinformatics)

Rocco Varela: An inhibitor of NEDD8-activating enzyme as a new approach to treat cancer Nature. 2009 Apr 9;458(7239):732-6

6/2/09 Make-Up Day

Academic YEAR 2008

Date Speaker 1 Speaker 2 Details
10/9/07 Maya Chandru (Biophysics) Brianna Burden (CCB)

Maya Chandru (Biophysics)

Multi-step pericellular proteolysis controls the transition from individual to collective cancer cell invasion.

Wolf et al, Nat Cell Biol 2007 Aug 9

Brianna Burden (CCB)

Aptamer Displacement Identifies Alternative Small-Molecule Target Sites that Escape Viral Resistance

amazaki et al, Cell: Chemistry and Biology 14, 804-812, 2007.

10/16/07 Jeremy Phillips (Bioinformatics) Reid Williams (Biophysics)

Jeremy Phillips (Bioinformatics)

Two distinct modes of guidance signalling during collective migration of border cells.

Bianco A, Poukkula M, Cliffe A, Mathieu J, Luque CM, Fulga TA, Rorth P. Nature. 2007 Jul 19;448(7151):362-5.

Reid Williams (Biophysics)

Selection and evolution of enzymes from a partially randomized non-catalytic scaffold

Seelig B, Szostak JW. Nature. 2007 Aug 16;448(7155):828-31.

10/23/07 Daniel Gray (CCB) Rebeca Choy (Biophysics)

Daniel Gray (CCB)

Crystal Structure of an Ancient Protein: Evolution by Conformational Epistasis.

Ortlund, Bridgham, Redinbo, Thornton. Science. 2007 Sep 14;317(5844):1544-8. Epub 2007 Aug 16.

http://www.nature.com/nsmb/journal/v14/n9/abs/nsmb1280.html

Rebeca Choy (Biophysics)

In vivo dynamics of RNA polymerase II transcription

Xavier Darzacq, Yaron Shav-Tal, Valeria de Turris, Yehuda Brody, Shailesh M Shenoy, Robert D Phair & Robert H Singer. Nature Structural & Molecular Biology - 14, 796 - 806 (2007).

10/30/07 Charles Biddle-Snead (Biophysics) Iana Serafimova (CCB)

Charles Biddle-Snead (Biophysics)

Array Tomography: A New Tool for Imaging the Molecular Architecture and Ultrastructure of Neural Circuits

Kristina D. Micheva and Stephen J Smith. Neuron 55

Iana Serafimova (CCB)

Splicing factor SF3b as a target of the antitumor natural product pladienolide

Yoshihiko Kotake1, Koji Sagane1, Takashi Owa, Yuko Mimori-Kiyosue, Hajime Shimizu, Mai Uesugi, Yasushi Ishihama, Masao Iwata & Yoshiharu Mizui. Nature Chemical Biology, Vol 3, Number 9, September 2007, p570 - 575.

11/6/07 Daniele Canzio (CCB) David Stanley (Biophysics)

Daniele Canzio (CCB)

A motor that makes his own track: helicase unwinding of DNA: Single-Molecule Studies Reveal Dynamics of DNA unwinding by the Ring-Shaped T7 Helicase

Cell 129, 1299-1309, June 29, 2007

David Stanley (Biophysics)

Dynamic Scaffolding of a G Protein-Coupled Signaling System

Prashant Mishra, Michael Socolich, Mark A. Wall, Jennifer Graves, ZiFen Wang, and Rama Ranganathan. Cell, Vol 131, 80-92, 05 October 2007

11/13/07 Kris Kuchenbecker (Biophysics)

Kris Kuchenbecker (Biophysics)

Energetics and dynamics of SNAREpin folding across lipid bilayers.

Nature Structural and Molecular biology. October 2007.

11/20/07 Laura Lavery (Biophysics) Sheel Dandekar (Biophysics)

Laura Lavery (Biophysics)

High-afinity single-domain binding proteins with a binary-code interface.

Akiko Koidea, Ryan N. Gilbreth, Kaori Esaki, Valentina Tershko, Shohei Koide. PNAS, Vol 104, No. 16. April 17, 2007.

http://www.pnas.org/cgi/content/full/104/16/6632

Sheel Dandekar (Biophysics)

Ordered phosphorylation governs oscillation of a three-protein circadian clock

Rust MJ, Markson JS, Lane WS, Fisher DS, O'Shea EK. Science. 2007 Nov 2;318(5851):809-12. Epub 2007 Oct 4.

1/8/08 Jonathan Choy (CCB) Sai Duriseti (Biophysics)

Jonathan Choy (CCB)

Design of Cyclic Peptides That Bind Protein Surfaces with Antibody-Like Affinity

Steven W. Millward, Stephen Fiacco, Ryan J. Austin, and Richard W. Roberts (2007) ACS Chem. Biol. 2, 625-634.

Sai Duriseti (Biophysics)

A Simple DNA-Based Translation System

Alejandra V. Garibotti, Shiping Liao, and Nadrian C. Seeman. Nano Letters 2007 Vol. 7, No. 2. 480-483.

1/15/08 Ryan Ritterson (Biophysics) Charles Kehoe (Bioinformatics)

Ryan Ritterson (Biophysics)

Retroposons: DNA parasites or facilitators? A CORE-SINE retroposon as a highly conserved neuronal enhancer.

Ancient Exaptation of a CORE-SINE Retroposon into a Highly Conserved Mammalian Neuronal Enhancer of the Proopiomelanocortin Gene. Santangelo AM, de Souza FSJ, Franchini LF, Bumaschny VF, Low MJ, et al. PLoS Genetics Vol. 3, No. 10, e166doi:10.1371/journal.pgen.0030166

http://genetics.plosjournals.org/perlserv/?request=get-document&amp;doi=10.1371/journal.pgen.0030166

Charles Kehoe (Bioinformatics)

Functional specificity among ribosomal proteins regulates gene expression.

Komili S, Farny NG, Roth FP, Silver PA.Cell. 2007 Nov 2;131(3):450-1.

1/22/08 David Booth (Biophysics)

David Booth (Biophysics)

Solvent Tuning of Electrochemical Potentials in the Active Sites of HiPIP Versus Ferredoxin

Solvent Tuning of Electrochemical Potentials in the Active Sites of HiPIP Versus Ferredoxin Abhishek Dey, Francis E. Jenney, Jr., Michael W. W. Adams, Elena Babini, Yasuhiro Takahashi, Keiichi Fukuyama, Keith O. Hodgson, Britt Hedman, Edward I. Solomon, Science, 318, 1464-8, 2007

1/29/08 Joseph Kliegman (Biophysics) Michael Lopez (CCB)

Joseph Kliegman (Biophysics)

Minor Details of Transcription Factor Specificity

Rohit Joshi, Jonathan M. Passner, Remo Rohs, Rinku Jain, Alona Sosinsky, Michael A. Crickmore, Vinitha Jacob, Aneel K. Aggarwal, Barry Honig and Richard S. Mann. Functional Specificity of a Hox Protein Mediated by the Recognition of Minor Groove Structure, CellVolume 131, Issue 3, , 2 November 2007, Pages 530-543.

Michael Lopez (CCB)

A GluR1-cGKII Interaction Regulates AMPA Receptor Trafficking

Yafell Serulle, Shuang Zhang, Ipe Ninan, Daniela Puzzo, Maria McCarthy, Latika Khatri, Ottavio Arancio, and Edward B. Ziff Neuron 56,

2/5/08 Noah Ollikainen (Bioinformatics) George Peterson (Biophysics)

Noah Ollikainen (Bioinformatics)

Somewhere over the brainbow

Jean Livet, Tamily A. Weissman, Hyuno Kang, Ryan W. Draft, Ju Lu, Robyn A. Bennis, Joshua R. Sanes & Jeff W. Lichtman. Transgenic strategies for combinatorial expression of fluorescent proteins in the nervous system. Nature. 450, 56-62 (2007).

http://www.nature.com/nature/journal/v450/n7166/abs/nature06293.html

George Peterson (Biophysics)

Nicotinamide Riboside Promotes Sir2 Silencing and Extends Lifespan via Nrk and Urh1/Pnp1/Meu1 Pathways to NAD+

Belenky P, Racette FG, Bogan KL, McClure JM, Smith JS, Brenner C. Cell 129: 473-84 (2007)

http://www.cell.com/content/article/abstract?uid=PIIS009286740700390X

2/12/08 Rebecca Maglathlin (CCB) Heather Newman (Biophysics)

Rebecca Maglathlin (CCB)

Structural Rearrangements of NR1/NR2A NMDA Receptors during Allosteric Inhibition

Marc Gielen, Anne Le Goff, David Stroebel, Jon W. Johnson, Jacques Neyton, and Pierre Paoletti. Neuron 57, 80 January 10, 2008

Heather Newman (Biophysics)

Multicolor Super-Resolution Imagining with Photo-switchable Fluorescent Probes

Multicolor Super-Resolution Imagining with Photo-switchable Fluorescent Probes Mark Bates et al., Science 317, 1749 (2007).

2/19/08 Peter Skewes-Cox (Bioinformatics) David Burkhardt (Biophysics)

Peter Skewes-Cox (Bioinformatics)

Will newly identified host factors exploited by HIV make good drug targets?

"Identification of Host Proteins Required for HIV Infection Through a Functional Genomic Screen," Abraham L. Brass, Derek M. Dykxhoorn, Yair Benita, Nan Yan, Alan Engelman, Ramnik J. Xavier, Judy Lieberman, Stephen J. Elledge. Science, 2008 Jan 10

David Burkhardt (Biophysics)

Switching from repression to activation: microRNAs can up-regulate translation.

Vasudevan S, Tong Y, Steitz JA, " Switching from repression to activation: microRNAs can up-regulate translation.", Science 2007 Dec 21

2/26/08 Hannes Braberg (Biophysics) Rand Miller (CCB)

Hannes Braberg (Biophysics)

High-content single-cell drug screening with phosphospecific flow cytometry

Peter O Krutzik, Janelle M Crane, Matthew R Clutter and Garry P Nolan. Nature Chemical Biology 4, 132-142 (2007) doi:10.1038/nchembio.2007.59

Rand Miller (CCB)

Systemic Leukocyte-Directed siRNA Delivery Revealing Cyclin D1 as an Anti-Inflammatory Target

Peer, D., Park, E. J., Morishita, Y., Carman, C. V., Shimaoka, M, "Systemic Leukocyte-Directed siRNA Delivery Revealing Cyclin D1 as an Anti-Inflammatory Target," /Science/, 319, 627-630, (2008). DOI: 10.1126/science.1149859

3/4/08 Nicholas Hertz (CCB) Elaine Kirschke (Biophysics)

Nicholas Hertz (CCB)

A Comprehensive Profile of Brain Enzymes that Hydrolyze the Endocannabinoid 2-Arachidonoylglycerol

Blankman, J.L., Simon, G.M., Cravatt, B.F. (2007). A Comprehensive Profile of Brain Enzymes that Hydrolyze the Endocannabinoid 2-Arachidonoylglycerol. Chem. Biol. 14, 1347-1356

Elaine Kirschke (Biophysics)

Activation of the Chaperone Hsp26 Is Controlled by the Rearrangement of Its Thermosensor Domain

T. Franzmann, P. Menhorn, S. Walter, and J. Buchner. (2008) Activation of the Chaperone Hsp26 Is Controlled by the Rearrangement of Its Thermosensor Domain. Molecular Cell, Vol 29, 207-216, 01

3/11/08 Bethany Simmons (Bioinformatics) Kiyoshi Egami (Biophysics)

Bethany Simmons (Bioinformatics)

Global analysis of mRNA localization reveals a prominent role in organizing cellular architecture and function.

Lecuyer E, Yoshida H, ..., Tomancak P, Krause HM Cell 2007 Oct 5 131(1):174-87

Kiyoshi Egami (Biophysics)

Glycan topology determines human adaptation of avian H5N1 virus hemagglutinin.

Chandrasekaran A, Srinivasan A, Raman R, Viswanathan K, Raguram S, Tumpey TM, Sasisekharan V, Sasisekharan R. Nat Biotechnol. 2008 Jan;26(1):107-13. Epub 2008 Jan 6.

4/1/08 Brandon Butler (CCB) Jaline Gerardin (Biophysics)

Brandon Butler (CCB)

A beta-arrestin 2 Signalling Complex Mediates Lithium Action on Behavior

Jean-Martin Beaulieu et al. Cell, 132, 125-136, Jan 11, 2008.

Jaline Gerardin (Biophysics)

Direct observation of hierarchical folding in single riboswitch aptamers

Greenleaf WJ, Frieda KL, Foster DAN, Woodside MT, Block SM. Direct observation of hierarchical folding in single riboswitch aptamers. Science. 2008 Feb 1;319(5863):630-3.

4/8/08 Carrie Shiau (CCB) Adam Marko (Bioinformatics)

Carrie Shiau (CCB)

Transcriptional repression mediated by repositioning of genes to the nuclear lamina

Reddy, K. L. et al. Transcriptional repression mediated by repositioning of genes to the nuclear lamina.

Adam Marko (Bioinformatics)

Computational Enzyme Design

Lin Jiang, Eric A. Althoff, Fernando R. Clemente, Lindsey Doyle, Daniela R??thlisberger, Alexandre Zanghellini, Jasmine L. Gallaher, Jamie L. Betker, Fujie Tanaka, Carlos F. Barbas, III, Donald Hilvert, Kendall N. Houk, Barry L. Stoddard, David Baker. De Novo Computational Design of Retro-Aldol Enzymes. Science 7 March 2008: Vol. 319. no. 5868, pp. 1387 - 139. DOI: 10.1126/science.1152692

4/15/08 Jennifer Hsiao (Biophysics) Jennifer Liu (CCB)

Jennifer Hsiao (Biophysics)

Hydrodynamic Flow-Mediated Protein Sorting on the Cell Surface of Trypanosomes

Markus Engstler, Thomas Pfohl, Stephan Herminghaus, Michael Boshart, Geert Wiegertjes, Niko Heddergott, and Peter Overath. Cell 131, 505- 515, November 2, 2007

Jennifer Liu (CCB)

Preserving cell shape under environmental stress

Boaz Cook, Robert W Hardy, William B McConnaughey, Charles S Zuker. Nature 452, 361-364 (20 March 2008), doi:10.1038/nature06603

4/22/08 Gabriel Rocklin (Biophysics) Cheryl Tajon (CCB)

Gabriel Rocklin (Biophysics)

Integrating high-content screening and ligand-target prediction to identify mechanism of action

Young, DW et al. Integrating high-content screening and ligand-target prediction to identify mechanism of action. Nature Chemical Biology 4:1 Jan 2008

Cheryl Tajon (CCB)

Near-Infrared Resonant Nanoshells for Combined Optical Imaging and Photothermal Cancer Therapy

Andre´ M. Gobin, Min Ho Lee, Naomi J. Halas, William D. James, Rebekah A. Drezek, and Jennifer L. West. Near-Infrared Resonant Nanoshells for Combined Optical Imaging and Photothermal Cancer Therapy. Nano Letters, 2007, vol. 7, no. 7, 1929-34.

4/29/08 Brittany Belin (Biophysics) Xiu Ming Wong (CCB)

Brittany Belin (Biophysics)

Structural basis of membrane invagination by F-BAR domains

Frost A, Perera R, Roux A, Spasov K, Destaing O, Egelman EH, De Camilli P, Unger VM. (2008) Structural basis of membrane invagination by F-BAR domains. Cell 132(5):807-17.

Xiu Ming Wong (CCB)

Ran-Binding Protein 3 Phosphorylation Links the Ras and PI3-Kinase Pathways to Nucleocytoplasmic Transport.

Sang-Oh Yoon, Sejeong Shin, Yuzhen Liu, Bryan A. Ballif, Michele S. Woo, Steven P. Gygi, and John Blenis, Ran-Binding Protein 3 Phosphorylation Links the Ras and PI3-Kinase Pathways to Nucleocytoplasmic Transport. Molecular Cell, Volume 29, Issue 3, 15 February 2008, Pages 362-375.

5/6/08 Monica Tremont (Biophysics) Christopher Wen (Bioinformatics)

Monica Tremont (Biophysics)

Allosteric cooperativity in protein kinase A

Masterson, L. Rl et al. Allosteric cooperativity in protein kinase A. Proc. Nat. Acad. Sci. U.S.A. 105(2), 506-511 (2008).

http://www.pnas.org/cgi/reprint/105/2/506

Christopher Wen (Bioinformatics)

1. Membrane proteins of the endoplasmic reticulum induce high-curvature tubules.

Hu J, Shibata Y, Voss C, Shemesh T, Li Z, Coughlin M, Kozlov MM, Rapoport TA, Prinz WA. Membrane proteins of the endoplasmic reticulum induce high-curvature tubules. Science. 2008 Feb 29;319(5867):1247-50

http://www.sciencemag.org/cgi/content/full/319/5867/1247

5/13/08 Marlisa Pillsbury (CCB) Robin Aglietti (CCB)

Marlisa Pillsbury (CCB)

Concurrent Fast and Slow Cycling of a Transcriptional Activator at an Endogenous Promoter

Karpova,T, Kim, MJ, Spriet, C, Nalley, K, Stasevich, TJ, Kherrouche, Z, Heliot, L, McNally JG. Concurrent Fast and Slow Cycling of a Transcriptional Activator at an Endogenous Promoter. Science 25 January 2008: Vol. 319. no. 5862, pp. 466 - 469. DOI: 10.1126/science.1150559

Robin Aglietti (CCB)

Structural Basis for Signal-Sequence Recognition by the Translocase Motor SecA as Determined by NMR

Ioannis Gelis, Alexandre M.J.J. Bonvin, Dimitra Keramisanou, Marina Koukaki, Giorgos Gouridis, Spyridoula Karamanou, Anastassios Economou, and Charalampos G. Kalodimos. Structural Basis for Signal-Sequence Recognition by the Translocase Motor SecA as Determined by NMR. Cell, Vol 131, 756-769, 16 November 2007

Academic YEAR 2007

Date Speaker 1 Speaker 2 Details
10/10/06 Segun Williams (CCB) Stephen Floor (Biophysics)
10/17/06 Michelle Dimon (Bioinformatics) Ethan Mirsky (Biophysics)

Michelle Dimon (Bioinformatics)

DNA Sequences Predict Packaging

Segal E, Fondufe-Mittendorf Y, Chen L, Thastrom AC, Field Y, Moore IK, Wang JPZ, Widome J. A genomic code for nucleosome positioning. Nature 17:442 (7104), 772 (2006)

Ethan Mirsky (Biophysics)

Oceanic Gene Pooling

Photosynthesis genes in marine viruses yield proteins during host infection. Nature. 438(7064): 86 (2005)

10/24/06 Hesper Rego (Biophysics) Karin Buser (CCB)
10/31/06 Rafaela Ferreira (CCB) Michael Cary (Bioinformatics)

Michael Cary (Bioinformatics)

The first genome-wide map of DNA methylation

Zhang X, Yazaki J, Sundaresan A, Cokus S, Chan SW, Chen H, Henderson IR, Shinn P, Pellegrini M, Jacobsen SE, Ecker JR. Genome-wide high-resolution mapping and functional analysis of DNA methylation in arabidopsis. Cell 126(6): 1189 (2006)

11/7/06 Benjamin Rhau (Biophysics) Andy MacKinnon (CCB)

Benjamin Rhau (Biophysics)

Computational redesign of endonuclease DNA binding and cleavage specificity.

Ashworth J, Hayranek JJ, Duarte CM, Sussman D, Monnat RJ Jr., Stoddard BL, Baker D. Nature. 2006 Jun 1;441(7093):656-9.

Andy MacKinnon (CCB)

A Proposed Twisting Mechanism of Dynamin During Membrane Fission

Roux, Aurelien, Uyhazi, Katherine, Frost, Adam, De Camilli, Pietro. GTP-dependent twisting of dynamin implicates constriction and tension in membrane fission.

11/14/06 Colin Smith (Bioinformatics) Bryant Chhun (Biophysics)

Colin Smith (Bioinformatics)

Taking turns with the whip

Leake MC, Chandler JH, Wadhams GH, Bai F, Berry RM, Armitage JP. Stoichiometry and turnover in single, functioning membrane protein complexes. Nature 443(7109):355 (2006)

11/21/06 Chris McClendon (Biophysics) Mark Borja (CCB)
1/9/07 Liz Montabana (Biophysics) David Barkan (Bioinformatics)

David Barkan (Bioinformatics)

Imitation by epidermal growth factor receptor is the sincerest form of flattery

Zhang et al. An allosteric mechanism for activation of the kinase domain of epidermal growth factor receptor. Cell. 125 (6):1137-49. (2006)

1/16/07 Julie Zorn (CCB) Richard Oberdorf (Biophysics)
1/23/07 Deb Datta (Biophysics) Brandon Tavshanjian (CCB)
1/30/07 Beth Apsel (CCB) Leonard Apeltsin (Bioinformatics)

Leonard Apeltsin (Bioinformatics)

Computer Tobacco Mosaic Viruses: Engineering a Digital Memory Device from Biological Parts

Tseng, R.J. Tsai, C. Ma, L. Ouyang, J. Ozkan C.S. Yang, Y. Digitalmemory device based on tobacco mosaic virus conjugated with nanoparticles. Nature Nanotechnology. 1, 72-77. (2006)

2/6/07 Emily Crawford (CCB) Charles Biddle-Snead (Biophysics)
2/13/07 Jeremy Phillips (Bioinformatics) Maya Chandru (Biophysics)

Jeremy Phillips (Bioinformatics)

A noise-excitable circuit induces competence in B. subtilis

Suel GM, Garcia-Ojalvo J, Liberman LM, Elowitz MB. An excitable gene regulatory circuit induces transient cellular differentiation. Nature. 440(7083):545-50. (2006)

2/20/07 Ryan Ritterson (Biophysics) Briana Burden (CCB)
2/27/07 Daniel Gray (CCB) David Stanley (Biophysics)
3/6/07 Marlisa Pillsbury (CCB) David Stanley (Biophysics)
3/13/07 Reid Williams (Biophysics) Daniele Canzio (CCB)
3/20/07 Laura Lavery (Biophysics) Kimberly Erickson (CCB)
4/3/07 Iana Serafimova (CCB) Kris Kuchenbecker (Biophysics)

Iana Serafimova (CCB)

Live-cell imaging of enzyme-substrate interaction reveals spatial regulation of PTP1B.

Yudushkin IA, Schleifenbaum A., Kinkhabwala A, Neel BG, Schultz C, Bastiaens PI. European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, D-69117 Heidelberg, Germany.

Kris Kuchenbecker (Biophysics)

Coupling substrate and ion binding to extracellular gate of a sodium-dependent aspartate transporter.

Boudker O, Ryan RM, Yernool D, Shimamoto K, Gouaux E. Science. 2007 Jan 5;315(5808):115-9.

4/10/07 Sheel Dandekar (Biophysics) Rebeca Choy (Biophysics)

Rebeca Choy (Biophysics)

From Swimming to Walking with a Salamander Robot Driven by a Spinal Cord Model

Auke Jan Ijspeert,1* Alessandro Crespi,1 Dimitri Ryczko,2,3 Jean-Marie Cabelguen2,3. Science 9 March 2007: Vol. 315. no. 5817, pp. 1416 - 1420 DOI: 10.1126/science.1138353